Comparison of conventional and cadmium-zinc-telluride single-photon emission computed tomography for analysis of thallium-201 myocardial perfusion imaging: an exploratory study in normal databases for different ethnicities.

PubMed

Ishihara, Masaru; Onoguchi, Masahisa; Taniguchi, Yasuyo; Shibutani, Takayuki

2017-12-01

The aim of this study was to clarify the differences in thallium-201-chloride (thallium-201) myocardial perfusion imaging (MPI) scans evaluated by conventional anger-type single-photon emission computed tomography (conventional SPECT) versus cadmium-zinc-telluride SPECT (CZT SPECT) imaging in normal databases for different ethnic groups. MPI scans from 81 consecutive Japanese patients were examined using conventional SPECT and CZT SPECT and analyzed with the pre-installed quantitative perfusion SPECT (QPS) software. We compared the summed stress score (SSS), summed rest score (SRS), and summed difference score (SDS) for the two SPECT devices. For a normal MPI reference, we usually use Japanese databases for MPI created by the Japanese Society of Nuclear Medicine, which can be used with conventional SPECT but not with CZT SPECT. In this study, we used new Japanese normal databases constructed in our institution to compare conventional and CZT SPECT. Compared with conventional SPECT, CZT SPECT showed lower SSS (p < 0.001), SRS (p = 0.001), and SDS (p = 0.189) using the pre-installed SPECT database. In contrast, CZT SPECT showed no significant difference from conventional SPECT in QPS analysis using the normal databases from our institution. Myocardial perfusion analyses by CZT SPECT should be evaluated using normal databases based on the ethnic group being evaluated.

Development of Databases on Iodine in Foods and Dietary Supplements

PubMed Central

Ershow, Abby G.; Skeaff, Sheila A.; Merkel, Joyce M.; Pehrsson, Pamela R.

2018-01-01

Iodine is an essential micronutrient required for normal growth and neurodevelopment; thus, an adequate intake of iodine is particularly important for pregnant and lactating women, and throughout childhood. Low levels of iodine in the soil and groundwater are common in many parts of the world, often leading to diets that are low in iodine. Widespread salt iodization has eradicated severe iodine deficiency, but mild-to-moderate deficiency is still prevalent even in many developed countries. To understand patterns of iodine intake and to develop strategies for improving intake, it is important to characterize all sources of dietary iodine, and national databases on the iodine content of major dietary contributors (including foods, beverages, water, salts, and supplements) provide a key information resource. This paper discusses the importance of well-constructed databases on the iodine content of foods, beverages, and dietary supplements; the availability of iodine databases worldwide; and factors related to variability in iodine content that should be considered when developing such databases. We also describe current efforts in iodine database development in the United States, the use of iodine composition data to develop food fortification policies in New Zealand, and how iodine content databases might be used when considering the iodine intake and status of individuals and populations. PMID:29342090

Korean Database of Cerebral Palsy: A Report on Characteristics of Cerebral Palsy in South Korea

PubMed Central

2017-01-01

Objective To introduce the Korean Database of Cerebral Palsy (KDCP) and to provide the first report on characteristics of subjects with cerebral palsy (CP). Methods The KDCP is a nationwide database of subjects with CP, which includes a total of 773 subjects. Characteristics such as demography, birth history, onset and type of CP, brain magnetic resonance imaging (MRI) findings, functional ability and accompanying impairments, were extracted and analyzed. Results Preterm delivery and low birth weight were found in 59.51% and 60.28% of subjects, respectively. Postnatally acquired CP was 15.3%. The distribution of CP was 87.32%, 5.17%, and 1.81% for spastic, dyskinetic, and ataxic types, respectively. Functional ability was the worst in dyskinetic CP, as compared to other types of CP. Speech-language disorder (43.9%), ophthalmologic impairment (32.9%), and intellectual disability (30.3%) were the three most common accompanying impairments. The number of accompanying impairments was elevated in subjects with preterm birth and low birth weight. Brain MRI showed normal findings, malformations, and non-malformations in 10.62%, 9.56%, and 77.35% of subjects, respectively. Subjects with normal MRI findings had better functional ability than subjects with other MRI findings. MRI findings of a non-malformation origin, such as periventricular leukomalacia, were more common in subjects with preterm birth and low birth weight. Conclusion The KDCP and its first report are introduced in this report, wherein the KDCP established agreement on terminologies of CP. This study added information on the characteristics of subjects with CP in South Korea, which can now be compared to those of other countries and ethnicities. PMID:28971049

Functional integration of automated system databases by means of artificial intelligence

NASA Astrophysics Data System (ADS)

Dubovoi, Volodymyr M.; Nikitenko, Olena D.; Kalimoldayev, Maksat; Kotyra, Andrzej; Gromaszek, Konrad; Iskakova, Aigul

2017-08-01

The paper presents approaches for functional integration of automated system databases by means of artificial intelligence. The peculiarities of turning to account the database in the systems with the usage of a fuzzy implementation of functions were analyzed. Requirements for the normalization of such databases were defined. The question of data equivalence in conditions of uncertainty and collisions in the presence of the databases functional integration is considered and the model to reveal their possible occurrence is devised. The paper also presents evaluation method of standardization of integrated database normalization.

Image database for digital hand atlas

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente; Dey, Partha S.; Gertych, Arkadiusz; Pospiech-Kurkowska, Sywia

2003-05-01

Bone age assessment is a procedure frequently performed in pediatric patients to evaluate their growth disorder. A commonly used method is atlas matching by a visual comparison of a hand radiograph with a small reference set of old Greulich-Pyle atlas. We have developed a new digital hand atlas with a large set of clinically normal hand images of diverse ethnic groups. In this paper, we will present our system design and implementation of the digital atlas database to support the computer-aided atlas matching for bone age assessment. The system consists of a hand atlas image database, a computer-aided diagnostic (CAD) software module for image processing and atlas matching, and a Web user interface. Users can use a Web browser to push DICOM images, directly or indirectly from PACS, to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, are then extracted and compared with patterns from the atlas image database to assess the bone age. The digital atlas method built on a large image database and current Internet technology provides an alternative to supplement or replace the traditional one for a quantitative, accurate and cost-effective assessment of bone age.

Big data in sleep medicine: prospects and pitfalls in phenotyping

PubMed Central

Bianchi, Matt T; Russo, Kathryn; Gabbidon, Harriett; Smith, Tiaundra; Goparaju, Balaji; Westover, M Brandon

2017-01-01

Clinical polysomnography (PSG) databases are a rich resource in the era of “big data” analytics. We explore the uses and potential pitfalls of clinical data mining of PSG using statistical principles and analysis of clinical data from our sleep center. We performed retrospective analysis of self-reported and objective PSG data from adults who underwent overnight PSG (diagnostic tests, n=1835). Self-reported symptoms overlapped markedly between the two most common categories, insomnia and sleep apnea, with the majority reporting symptoms of both disorders. Standard clinical metrics routinely reported on objective data were analyzed for basic properties (missing values, distributions), pairwise correlations, and descriptive phenotyping. Of 41 continuous variables, including clinical and PSG derived, none passed testing for normality. Objective findings of sleep apnea and periodic limb movements were common, with 51% having an apnea–hypopnea index (AHI) >5 per hour and 25% having a leg movement index >15 per hour. Different visualization methods are shown for common variables to explore population distributions. Phenotyping methods based on clinical databases are discussed for sleep architecture, sleep apnea, and insomnia. Inferential pitfalls are discussed using the current dataset and case examples from the literature. The increasing availability of clinical databases for large-scale analytics holds important promise in sleep medicine, especially as it becomes increasingly important to demonstrate the utility of clinical testing methods in management of sleep disorders. Awareness of the strengths, as well as caution regarding the limitations, will maximize the productive use of big data analytics in sleep medicine. PMID:28243157

A study of the very high order natural user language (with AI capabilities) for the NASA space station common module

NASA Technical Reports Server (NTRS)

Gill, E. N.

1986-01-01

The requirements are identified for a very high order natural language to be used by crew members on board the Space Station. The hardware facilities, databases, realtime processes, and software support are discussed. The operations and capabilities that will be required in both normal (routine) and abnormal (nonroutine) situations are evaluated. A structure and syntax for an interface (front-end) language to satisfy the above requirements are recommended.

Lognormal Behavior of the Size Distributions of Animation Characters

NASA Astrophysics Data System (ADS)

Yamamoto, Ken

This study investigates the statistical property of the character sizes of animation, superhero series, and video game. By using online databases of Pokémon (video game) and Power Rangers (superhero series), the height and weight distributions are constructed, and we find that the weight distributions of Pokémon and Zords (robots in Power Rangers) follow the lognormal distribution in common. For the theoretical mechanism of this lognormal behavior, the combination of the normal distribution and the Weber-Fechner law is proposed.

MICA: desktop software for comprehensive searching of DNA databases

PubMed Central

Stokes, William A; Glick, Benjamin S

2006-01-01

Background Molecular biologists work with DNA databases that often include entire genomes. A common requirement is to search a DNA database to find exact matches for a nondegenerate or partially degenerate query. The software programs available for such purposes are normally designed to run on remote servers, but an appealing alternative is to work with DNA databases stored on local computers. We describe a desktop software program termed MICA (K-Mer Indexing with Compact Arrays) that allows large DNA databases to be searched efficiently using very little memory. Results MICA rapidly indexes a DNA database. On a Macintosh G5 computer, the complete human genome could be indexed in about 5 minutes. The indexing algorithm recognizes all 15 characters of the DNA alphabet and fully captures the information in any DNA sequence, yet for a typical sequence of length L, the index occupies only about 2L bytes. The index can be searched to return a complete list of exact matches for a nondegenerate or partially degenerate query of any length. A typical search of a long DNA sequence involves reading only a small fraction of the index into memory. As a result, searches are fast even when the available RAM is limited. Conclusion MICA is suitable as a search engine for desktop DNA analysis software. PMID:17018144

BioWarehouse: a bioinformatics database warehouse toolkit

PubMed Central

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David WJ; Tenenbaum, Jessica D; Karp, Peter D

2006-01-01

Background This article addresses the problem of interoperation of heterogeneous bioinformatics databases. Results We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. Conclusion BioWarehouse embodies significant progress on the database integration problem for bioinformatics. PMID:16556315

BioWarehouse: a bioinformatics database warehouse toolkit.

PubMed

Lee, Thomas J; Pouliot, Yannick; Wagner, Valerie; Gupta, Priyanka; Stringer-Calvert, David W J; Tenenbaum, Jessica D; Karp, Peter D

2006-03-23

This article addresses the problem of interoperation of heterogeneous bioinformatics databases. We introduce BioWarehouse, an open source toolkit for constructing bioinformatics database warehouses using the MySQL and Oracle relational database managers. BioWarehouse integrates its component databases into a common representational framework within a single database management system, thus enabling multi-database queries using the Structured Query Language (SQL) but also facilitating a variety of database integration tasks such as comparative analysis and data mining. BioWarehouse currently supports the integration of a pathway-centric set of databases including ENZYME, KEGG, and BioCyc, and in addition the UniProt, GenBank, NCBI Taxonomy, and CMR databases, and the Gene Ontology. Loader tools, written in the C and JAVA languages, parse and load these databases into a relational database schema. The loaders also apply a degree of semantic normalization to their respective source data, decreasing semantic heterogeneity. The schema supports the following bioinformatics datatypes: chemical compounds, biochemical reactions, metabolic pathways, proteins, genes, nucleic acid sequences, features on protein and nucleic-acid sequences, organisms, organism taxonomies, and controlled vocabularies. As an application example, we applied BioWarehouse to determine the fraction of biochemically characterized enzyme activities for which no sequences exist in the public sequence databases. The answer is that no sequence exists for 36% of enzyme activities for which EC numbers have been assigned. These gaps in sequence data significantly limit the accuracy of genome annotation and metabolic pathway prediction, and are a barrier for metabolic engineering. Complex queries of this type provide examples of the value of the data warehousing approach to bioinformatics research. BioWarehouse embodies significant progress on the database integration problem for bioinformatics.

Analysis of differential protein expression in normal and neoplastic human breast epithelial cell lines

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

Williams, K.; Chubb, C.; Huberman, E.

High resolution two dimensional get electrophoresis (2DE) and database analysis was used to establish protein expression patterns for cultured normal human mammary epithelial cells and thirteen breast cancer cell lines. The Human Breast Epithelial Cell database contains the 2DE protein patterns, including relative protein abundances, for each cell line, plus a composite pattern that contains all the common and specifically expressed proteins from all the cell lines. Significant differences in protein expression, both qualitative and quantitative, were observed not only between normal cells and tumor cells, but also among the tumor cell lines. Eight percent of the consistently detected proteinsmore » were found in significantly (P < 0.001) variable levels among the cell lines. Using a combination of immunostaining, comigration with purified protein, subcellular fractionation, and amino-terminal protein sequencing, we identified a subset of the differentially expressed proteins. These identified proteins include the cytoskeletal proteins actin, tubulin, vimentin, and cytokeratins. The cell lines can be classified into four distinct groups based on their intermediate filament protein profile. We also identified heat shock proteins; hsp27, hsp60, and hsp70 varied in abundance and in some cases in the relative phosphorylation levels among the cell lines. Finally, we identified IMP dehydrogenase in each of the cell lines, and found the levels of this enzyme in the tumor cell lines elevated 2- to 20-fold relative to the levels in normal cells.« less

Database management systems for process safety.

PubMed

Early, William F

2006-03-17

Several elements of the process safety management regulation (PSM) require tracking and documentation of actions; process hazard analyses, management of change, process safety information, operating procedures, training, contractor safety programs, pre-startup safety reviews, incident investigations, emergency planning, and compliance audits. These elements can result in hundreds of actions annually that require actions. This tracking and documentation commonly is a failing identified in compliance audits, and is difficult to manage through action lists, spreadsheets, or other tools that are comfortably manipulated by plant personnel. This paper discusses the recent implementation of a database management system at a chemical plant and chronicles the improvements accomplished through the introduction of a customized system. The system as implemented modeled the normal plant workflows, and provided simple, recognizable user interfaces for ease of use.

Large-Scale Event Extraction from Literature with Multi-Level Gene Normalization

PubMed Central

Wei, Chih-Hsuan; Hakala, Kai; Pyysalo, Sampo; Ananiadou, Sophia; Kao, Hung-Yu; Lu, Zhiyong; Salakoski, Tapio; Van de Peer, Yves; Ginter, Filip

2013-01-01

Text mining for the life sciences aims to aid database curation, knowledge summarization and information retrieval through the automated processing of biomedical texts. To provide comprehensive coverage and enable full integration with existing biomolecular database records, it is crucial that text mining tools scale up to millions of articles and that their analyses can be unambiguously linked to information recorded in resources such as UniProt, KEGG, BioGRID and NCBI databases. In this study, we investigate how fully automated text mining of complex biomolecular events can be augmented with a normalization strategy that identifies biological concepts in text, mapping them to identifiers at varying levels of granularity, ranging from canonicalized symbols to unique gene and proteins and broad gene families. To this end, we have combined two state-of-the-art text mining components, previously evaluated on two community-wide challenges, and have extended and improved upon these methods by exploiting their complementary nature. Using these systems, we perform normalization and event extraction to create a large-scale resource that is publicly available, unique in semantic scope, and covers all 21.9 million PubMed abstracts and 460 thousand PubMed Central open access full-text articles. This dataset contains 40 million biomolecular events involving 76 million gene/protein mentions, linked to 122 thousand distinct genes from 5032 species across the full taxonomic tree. Detailed evaluations and analyses reveal promising results for application of this data in database and pathway curation efforts. The main software components used in this study are released under an open-source license. Further, the resulting dataset is freely accessible through a novel API, providing programmatic and customized access (http://www.evexdb.org/api/v001/). Finally, to allow for large-scale bioinformatic analyses, the entire resource is available for bulk download from http://evexdb.org/download/, under the Creative Commons – Attribution – Share Alike (CC BY-SA) license. PMID:23613707

Building a medical image processing algorithm verification database

NASA Astrophysics Data System (ADS)

Brown, C. Wayne

2000-06-01

The design of a database containing head Computed Tomography (CT) studies is presented, along with a justification for the database's composition. The database will be used to validate software algorithms that screen normal head CT studies from studies that contain pathology. The database is designed to have the following major properties: (1) a size sufficient for statistical viability, (2) inclusion of both normal (no pathology) and abnormal scans, (3) inclusion of scans due to equipment malfunction, technologist error, and uncooperative patients, (4) inclusion of data sets from multiple scanner manufacturers, (5) inclusion of data sets from different gender and age groups, and (6) three independent diagnosis of each data set. Designed correctly, the database will provide a partial basis for FDA (United States Food and Drug Administration) approval of image processing algorithms for clinical use. Our goal for the database is the proof of viability of screening head CT's for normal anatomy using computer algorithms. To put this work into context, a classification scheme for 'computer aided diagnosis' systems is proposed.

Challenges to the Standardization of Burn Data Collection: A Call for Common Data Elements for Burn Care.

PubMed

Schneider, Jeffrey C; Chen, Liang; Simko, Laura C; Warren, Katherine N; Nguyen, Brian Phu; Thorpe, Catherine R; Jeng, James C; Hickerson, William L; Kazis, Lewis E; Ryan, Colleen M

2018-02-20

The use of common data elements (CDEs) is growing in medical research; CDEs have demonstrated benefit in maximizing the impact of existing research infrastructure and funding. However, the field of burn care does not have a standard set of CDEs. The objective of this study is to examine the extent of common data collected in current burn databases.This study examines the data dictionaries of six U.S. burn databases to ascertain the extent of common data. This was assessed from a quantitative and qualitative perspective. Thirty-two demographic and clinical data elements were examined. The number of databases that collect each data element was calculated. The data values for each data element were compared across the six databases for common terminology. Finally, the data prompts of the data elements were examined for common language and structure.Five (16%) of the 32 data elements are collected by all six burn databases; additionally, five data elements (16%) are present in only one database. Furthermore, there are considerable variations in data values and prompts used among the burn databases. Only one of the 32 data elements (age) contains the same data values across all databases.The burn databases examined show minimal evidence of common data. There is a need to develop CDEs and standardized coding to enhance interoperability of burn databases.

Two-dimensional electrophoretic profiling of normal human kidney glomerulus proteome and construction of an extensible markup language (XML)-based database.

PubMed

Yoshida, Yutaka; Miyazaki, Kenji; Kamiie, Junichi; Sato, Masao; Okuizumi, Seiji; Kenmochi, Akihisa; Kamijo, Ken'ichi; Nabetani, Takuji; Tsugita, Akira; Xu, Bo; Zhang, Ying; Yaoita, Eishin; Osawa, Tetsuo; Yamamoto, Tadashi

2005-03-01

To contribute to physiology and pathophysiology of the glomerulus of human kidney, we have launched a proteomic study of human glomerulus, and compiled a profile of proteins expressed in the glomerulus of normal human kidney by two-dimensional gel electrophoresis (2-DE) and identification with matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) and/or liquid chromatography-tandem mass spectrometry (LC-MS/MS). Kidney cortices with normal appearance were obtained from patients under surgical nephrectomy due to renal tumor, and glomeruli were highly purified by a standard sieving method followed by picking-up under a phase-contrast microscope. The glomerular proteins were separated by 2-DE with 24 cm immobilized pH gradient strips in the 3-10 range in the first dimension and 26 x 20 cm sodium dodecyl sulfate polyacrylamide electrophoresis gels of 12.5% in the second dimension. Gels were silver-stained, and valid spots were processed for identification through an integrated robotic system that consisted of a spot picker, an in-gel digester, and a MALDI-TOF MS and / or a LC-MS/MS. From 2-DE gel images of glomeruli of four subjects with no apparent pathologic manifestations, a synthetic gel image of normal glomerular proteins was created. The synthetic gel image contained 1713 valid spots, of which 1559 spots were commonly observed in the respective 2-DE gels. Among the 1559 spots, 347 protein spots, representing 212 proteins, have so far been identified, and used for the construction of an extensible markup language (XML)-based database. The database is deposited on a web site (http://www.sw.nec.co.jp/bio/rd/hgldb/index.html) in a form accessible to researchers to contribute to proteomic studies of human glomerulus in health and disease.

Comparison of the calculation QRS angle for bundle branch block detection

NASA Astrophysics Data System (ADS)

Goeirmanto, L.; Mengko, R.; Rajab, T. L.

2016-04-01

QRS angle represent condition of blood circulation in the heart. Normally QRS angle is between -30 until 90 degree. Left Axis Defiation (LAD) and Right Axis Defiation (RAD) are abnormality conditions that lead to Bundle Branch Block. QRS angle is calculated using common method from physicians and compared to mathematical method using difference amplitudos and difference areas. We analyzed the standard 12 lead electrocardiogram data from MITBIH physiobank database. All methods using lead I and lead avF produce similar QRS angle and right QRS axis quadrant. QRS angle from mathematical method using difference areas is close to common method from physician. Mathematical method using difference areas can be used as a trigger for detecting heart condition.

CT-based attenuation correction and resolution compensation for I-123 IMP brain SPECT normal database: a multicenter phantom study.

PubMed

Inui, Yoshitaka; Ichihara, Takashi; Uno, Masaki; Ishiguro, Masanobu; Ito, Kengo; Kato, Katsuhiko; Sakuma, Hajime; Okazawa, Hidehiko; Toyama, Hiroshi

2018-06-01

Statistical image analysis of brain SPECT images has improved diagnostic accuracy for brain disorders. However, the results of statistical analysis vary depending on the institution even when they use a common normal database (NDB), due to different intrinsic spatial resolutions or correction methods. The present study aimed to evaluate the correction of spatial resolution differences between equipment and examine the differences in skull bone attenuation to construct a common NDB for use in multicenter settings. The proposed acquisition and processing protocols were those routinely used at each participating center with additional triple energy window (TEW) scatter correction (SC) and computed tomography (CT) based attenuation correction (CTAC). A multicenter phantom study was conducted on six imaging systems in five centers, with either single photon emission computed tomography (SPECT) or SPECT/CT, and two brain phantoms. The gray/white matter I-123 activity ratio in the brain phantoms was 4, and they were enclosed in either an artificial adult male skull, 1300 Hounsfield units (HU), a female skull, 850 HU, or an acrylic cover. The cut-off frequency of the Butterworth filters was adjusted so that the spatial resolution was unified to a 17.9 mm full width at half maximum (FWHM), that of the lowest resolution system. The gray-to-white matter count ratios were measured from SPECT images and compared with the actual activity ratio. In addition, mean, standard deviation and coefficient of variation images were calculated after normalization and anatomical standardization to evaluate the variability of the NDB. The gray-to-white matter count ratio error without SC and attenuation correction (AC) was significantly larger for higher bone densities (p < 0.05). The count ratio error with TEW and CTAC was approximately 5% regardless of bone density. After adjustment of the spatial resolution in the SPECT images, the variability of the NDB decreased and was comparable to that of the NDB without correction. The proposed protocol showed potential for constructing an appropriate common NDB from SPECT images with SC, AC and spatial resolution compensation.

pGenN, a gene normalization tool for plant genes and proteins in scientific literature.

PubMed

Ding, Ruoyao; Arighi, Cecilia N; Lee, Jung-Youn; Wu, Cathy H; Vijay-Shanker, K

2015-01-01

Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/).

Striving to live a normal life: a review of children and young people's experience of feeling different when living with a long term condition.

PubMed

Lambert, Veronica; Keogh, Deborah

2015-01-01

This paper presents a review of findings from qualitative studies on children's experience of feeling different when living with the long term conditions; diabetes, epilepsy and asthma. Following electronic database and hand searches of reference lists of identified papers, eighteen studies were selected for inclusion in the review. These studies revealed three common themes; participation in everyday life-restrictions and adjustments; treatment regimens-constraining and enabling; and communication-disclosure, stigma and support. Across these themes it was evident that children felt different physically and socially and they grappled constantly with balancing the dilemma of feeling and acting normal or feeling, being and revealing difference. Copyright © 2015 Elsevier Inc. All rights reserved.

Drug Use Normalization: A Systematic and Critical Mixed-Methods Review.

PubMed

Sznitman, Sharon R; Taubman, Danielle S

2016-09-01

Drug use normalization, which is a process whereby drug use becomes less stigmatized and more accepted as normative behavior, provides a conceptual framework for understanding contemporary drug issues and changes in drug use trends. Through a mixed-methods systematic review of the normalization literature, this article seeks to (a) critically examine how the normalization framework has been applied in empirical research and (b) make recommendations for future research in this area. Twenty quantitative, 26 qualitative, and 4 mixed-methods studies were identified through five electronic databases and reference lists of published studies. Studies were assessed for relevance, study characteristics, quality, and aspects of normalization examined. None of the studies applied the most rigorous research design (experiments) or examined all of the originally proposed normalization dimensions. The most commonly assessed dimension of drug use normalization was "experimentation." In addition to the original dimensions, the review identified the following new normalization dimensions in the literature: (a) breakdown of demographic boundaries and other risk factors in relation to drug use; (b) de-normalization; (c) drug use as a means to achieve normal goals; and (d) two broad forms of micro-politics associated with managing the stigma of illicit drug use: assimilative and transformational normalization. Further development in normalization theory and methodology promises to provide researchers with a novel framework for improving our understanding of drug use in contemporary society. Specifically, quasi-experimental designs that are currently being made feasible by swift changes in cannabis policy provide researchers with new and improved opportunities to examine normalization processes.

Automatic detection of anomalies in screening mammograms

PubMed Central

2013-01-01

Background Diagnostic performance in breast screening programs may be influenced by the prior probability of disease. Since breast cancer incidence is roughly half a percent in the general population there is a large probability that the screening exam will be normal. That factor may contribute to false negatives. Screening programs typically exhibit about 83% sensitivity and 91% specificity. This investigation was undertaken to determine if a system could be developed to pre-sort screening-images into normal and suspicious bins based on their likelihood to contain disease. Wavelets were investigated as a method to parse the image data, potentially removing confounding information. The development of a classification system based on features extracted from wavelet transformed mammograms is reported. Methods In the multi-step procedure images were processed using 2D discrete wavelet transforms to create a set of maps at different size scales. Next, statistical features were computed from each map, and a subset of these features was the input for a concerted-effort set of naïve Bayesian classifiers. The classifier network was constructed to calculate the probability that the parent mammography image contained an abnormality. The abnormalities were not identified, nor were they regionalized. The algorithm was tested on two publicly available databases: the Digital Database for Screening Mammography (DDSM) and the Mammographic Images Analysis Society’s database (MIAS). These databases contain radiologist-verified images and feature common abnormalities including: spiculations, masses, geometric deformations and fibroid tissues. Results The classifier-network designs tested achieved sensitivities and specificities sufficient to be potentially useful in a clinical setting. This first series of tests identified networks with 100% sensitivity and up to 79% specificity for abnormalities. This performance significantly exceeds the mean sensitivity reported in literature for the unaided human expert. Conclusions Classifiers based on wavelet-derived features proved to be highly sensitive to a range of pathologies, as a result Type II errors were nearly eliminated. Pre-sorting the images changed the prior probability in the sorted database from 37% to 74%. PMID:24330643

pGenN, a Gene Normalization Tool for Plant Genes and Proteins in Scientific Literature

PubMed Central

Ding, Ruoyao; Arighi, Cecilia N.; Lee, Jung-Youn; Wu, Cathy H.; Vijay-Shanker, K.

2015-01-01

Background Automatically detecting gene/protein names in the literature and connecting them to databases records, also known as gene normalization, provides a means to structure the information buried in free-text literature. Gene normalization is critical for improving the coverage of annotation in the databases, and is an essential component of many text mining systems and database curation pipelines. Methods In this manuscript, we describe a gene normalization system specifically tailored for plant species, called pGenN (pivot-based Gene Normalization). The system consists of three steps: dictionary-based gene mention detection, species assignment, and intra species normalization. We have developed new heuristics to improve each of these phases. Results We evaluated the performance of pGenN on an in-house expertly annotated corpus consisting of 104 plant relevant abstracts. Our system achieved an F-value of 88.9% (Precision 90.9% and Recall 87.2%) on this corpus, outperforming state-of-art systems presented in BioCreative III. We have processed over 440,000 plant-related Medline abstracts using pGenN. The gene normalization results are stored in a local database for direct query from the pGenN web interface (proteininformationresource.org/pgenn/). The annotated literature corpus is also publicly available through the PIR text mining portal (proteininformationresource.org/iprolink/). PMID:26258475

Accounting for the Benefits of Database Normalization

ERIC Educational Resources Information Center

Wang, Ting J.; Du, Hui; Lehmann, Constance M.

2010-01-01

This paper proposes a teaching approach to reinforce accounting students' understanding of the concept of database normalization. Unlike a conceptual approach shown in most of the AIS textbooks, this approach involves with calculations and reconciliations with which accounting students are familiar because the methods are frequently used in…

Efficient data management tools for the heterogeneous big data warehouse

NASA Astrophysics Data System (ADS)

Alekseev, A. A.; Osipova, V. V.; Ivanov, M. A.; Klimentov, A.; Grigorieva, N. V.; Nalamwar, H. S.

2016-09-01

The traditional RDBMS has been consistent for the normalized data structures. RDBMS served well for decades, but the technology is not optimal for data processing and analysis in data intensive fields like social networks, oil-gas industry, experiments at the Large Hadron Collider, etc. Several challenges have been raised recently on the scalability of data warehouse like workload against the transactional schema, in particular for the analysis of archived data or the aggregation of data for summary and accounting purposes. The paper evaluates new database technologies like HBase, Cassandra, and MongoDB commonly referred as NoSQL databases for handling messy, varied and large amount of data. The evaluation depends upon the performance, throughput and scalability of the above technologies for several scientific and industrial use-cases. This paper outlines the technologies and architectures needed for processing Big Data, as well as the description of the back-end application that implements data migration from RDBMS to NoSQL data warehouse, NoSQL database organization and how it could be useful for further data analytics.

Quantitative assessment of motor fatigue: normative values and comparison with prior-polio patients.

PubMed

Meldrum, Dara; Cahalane, Eibhlis; Conroy, Ronan; Guthrie, Richard; Hardiman, Orla

2007-06-01

Motor fatigue is a common complaint of polio survivors and has a negative impact on activities of daily living. The aim of this study was to establish a normative database for hand grip strength and fatigue and to investigate differences between prior-polio subjects and normal controls. Static and dynamic hand grip fatigue and maximum voluntary isometric contraction (MVIC) of hand grip were measured in subjects with a prior history of polio (n = 44) and healthy controls (n = 494). A normative database of fatigue was developed using four indices of analysis. Compared with healthy controls, subjects with prior polio had significantly reduced hand grip strength but developed greater hand grip fatigue in only one fatigue index. Quantitative measurement of fatigue in the prior-polio population may be useful in order to detect change over time and to evaluate treatment strategies.

Expert system development for commonality analysis in space programs

NASA Technical Reports Server (NTRS)

Yeager, Dorian P.

1987-01-01

This report is a combination of foundational mathematics and software design. A mathematical model of the Commonality Analysis problem was developed and some important properties discovered. The complexity of the problem is described herein and techniques, both deterministic and heuristic, for reducing that complexity are presented. Weaknesses are pointed out in the existing software (System Commonality Analysis Tool) and several improvements are recommended. It is recommended that: (1) an expert system for guiding the design of new databases be developed; (2) a distributed knowledge base be created and maintained for the purpose of encoding the commonality relationships between design items in commonality databases; (3) a software module be produced which automatically generates commonality alternative sets from commonality databases using the knowledge associated with those databases; and (4) a more complete commonality analysis module be written which is capable of generating any type of feasible solution.

Adaptive non-local smoothing-based weberface for illumination-insensitive face recognition

NASA Astrophysics Data System (ADS)

Yao, Min; Zhu, Changming

2017-07-01

Compensating the illumination of a face image is an important process to achieve effective face recognition under severe illumination conditions. This paper present a novel illumination normalization method which specifically considers removing the illumination boundaries as well as reducing the regional illumination. We begin with the analysis of the commonly used reflectance model and then expatiate the hybrid usage of adaptive non-local smoothing and the local information coding based on Weber's law. The effectiveness and advantages of this combination are evidenced visually and experimentally. Results on Extended YaleB database show its better performance than several other famous methods.

Calibrating the coordination chemistry tool chest: metrics of bi- and tridentate ligands.

PubMed

Aguilà, David; Escribano, Esther; Speed, Saskia; Talancón, Daniel; Yermán, Luis; Alvarez, Santiago

2009-09-07

Bi- and multidentate ligands form part of the tools commonly used for designing coordination and supramolecular complexes with desired stereochemistries. Parameters and concepts usually employed include the normalized bite of bidentate ligands, their cis- or trans-coordinating ability, their rigidity or flexibility, or the duality of some ligands that can act in chelating or dinucleating modes. In this contribution we present a structural database study of over one hundred bi- and tridentate ligands that allows us to parametrize their coordinating properties and discuss the relevance of such parameters for the choice of coordination polyhedron or coordination sites.

Looking for Cancer Clues in Publicly Accessible Databases

PubMed Central

Lemkin, Peter F.; Smythers, Gary W.; Munroe, David J.

2004-01-01

What started out as a mere attempt to tentatively identify proteins in experimental cancer-related 2D-PAGE maps developed into VIRTUAL2D, a web-accessible repository for theoretical pI/MW charts for 92 organisms. Using publicly available expression data, we developed a collection of tissue-specific plots based on differential gene expression between normal and diseased states. We use this comparative cancer proteomics knowledge base, known as the tissue molecular anatomy project (TMAP), to uncover threads of cancer markers common to several types of cancer and to relate this information to established biological pathways. PMID:18629065

Looking for cancer clues in publicly accessible databases.

PubMed

Medjahed, Djamel; Lemkin, Peter F; Smythers, Gary W; Munroe, David J

2004-01-01

What started out as a mere attempt to tentatively identify proteins in experimental cancer-related 2D-PAGE maps developed into VIRTUAL2D, a web-accessible repository for theoretical pI/MW charts for 92 organisms. Using publicly available expression data, we developed a collection of tissue-specific plots based on differential gene expression between normal and diseased states. We use this comparative cancer proteomics knowledge base, known as the tissue molecular anatomy project (TMAP), to uncover threads of cancer markers common to several types of cancer and to relate this information to established biological pathways.

Prevalence of extracranial carotid artery aneurysms in patients with an intracranial aneurysm.

PubMed

Pourier, V E C; van Laarhoven, C J H C M; Vergouwen, M D I; Rinkel, G J E; de Borst, Gert J

2017-01-01

Aneurysms in various arterial beds have common risk- and genetic factors. Data on the correlation of extracranial carotid artery aneurysms (ECAA) with aneurysms in other vascular territories are lacking. We aimed to investigate the prevalence of ECAA in patients with an intracranial aneurysm (IA). We used prospectively collected databases of consecutive patients registered at the University Medical Center Utrecht with an unruptured intracranial aneurysm (UIA) or aneurysmal Subarachnoid hemorrhage (SAH). The medical files of patients included in both databases were screened for availability of radiological reports, imaging of the brain and of the cervical carotid arteries. All available radiological images were then reviewed primarily for the presence of an ECAA and secondarily for an extradural/cavernous carotid or vertebral artery aneurysm. An ECAA was defined as a fusiform dilation ≥150% of the normal internal or common carotid artery or a saccular distention of any size. We screened 4465 patient records (SAH database n = 3416, UIA database n = 1049), of which 2931 had radiological images of the carotid arteries available. An ECAA was identified in 12/638 patients (1.9%; 95% CI 1.1-3.3) with completely imaged carotid arteries and in 15/2293 patients (0.7%; 95% CI 0.4-1.1) with partially depicted carotid arteries. Seven out of 27 patients had an additional extradural (cavernous or vertebral artery) aneurysm. This comprehensive study suggests a prevalence for ECAA of approximately 2% of patients with an IA. The rarity of the disease makes screening unnecessary so far. Future registry studies should study the factors associated with IA and ECAA to estimate the prevalence of ECAA in these young patients more accurately.

GenColors-based comparative genome databases for small eukaryotic genomes.

PubMed

Felder, Marius; Romualdi, Alessandro; Petzold, Andreas; Platzer, Matthias; Sühnel, Jürgen; Glöckner, Gernot

2013-01-01

Many sequence data repositories can give a quick and easily accessible overview on genomes and their annotations. Less widespread is the possibility to compare related genomes with each other in a common database environment. We have previously described the GenColors database system (http://gencolors.fli-leibniz.de) and its applications to a number of bacterial genomes such as Borrelia, Legionella, Leptospira and Treponema. This system has an emphasis on genome comparison. It combines data from related genomes and provides the user with an extensive set of visualization and analysis tools. Eukaryote genomes are normally larger than prokaryote genomes and thus pose additional challenges for such a system. We have, therefore, adapted GenColors to also handle larger datasets of small eukaryotic genomes and to display eukaryotic gene structures. Further recent developments include whole genome views, genome list options and, for bacterial genome browsers, the display of horizontal gene transfer predictions. Two new GenColors-based databases for two fungal species (http://fgb.fli-leibniz.de) and for four social amoebas (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a single entry point for related genomes for the amoebozoa and fungal research communities and other interested users. Comparative genomics approaches are greatly facilitated by these resources.

Damming the genomic data flood using a comprehensive analysis and storage data structure

PubMed Central

Bouffard, Marc; Phillips, Michael S.; Brown, Andrew M.K.; Marsh, Sharon; Tardif, Jean-Claude; van Rooij, Tibor

2010-01-01

Data generation, driven by rapid advances in genomic technologies, is fast outpacing our analysis capabilities. Faced with this flood of data, more hardware and software resources are added to accommodate data sets whose structure has not specifically been designed for analysis. This leads to unnecessarily lengthy processing times and excessive data handling and storage costs. Current efforts to address this have centered on developing new indexing schemas and analysis algorithms, whereas the root of the problem lies in the format of the data itself. We have developed a new data structure for storing and analyzing genotype and phenotype data. By leveraging data normalization techniques, database management system capabilities and the use of a novel multi-table, multidimensional database structure we have eliminated the following: (i) unnecessarily large data set size due to high levels of redundancy, (ii) sequential access to these data sets and (iii) common bottlenecks in analysis times. The resulting novel data structure horizontally divides the data to circumvent traditional problems associated with the use of databases for very large genomic data sets. The resulting data set required 86% less disk space and performed analytical calculations 6248 times faster compared to a standard approach without any loss of information. Database URL: http://castor.pharmacogenomics.ca PMID:21159730

West Virginia yellow-poplar lumber defect database

Treesearch

Lawrence E. Osborn; Charles J. Gatchell; Curt C. Hassler; Curt C. Hassler

1992-01-01

Describes the data collection methods and the format of the new West Virginia yellow-poplar lumber defect database that was developed for use with computer simulation programs. The database contains descriptions of 627 boards, totaling approximately 3,800 board. feet, collected in West Virginia in grades FAS, FASlF, No. 1 Common, No. 2A Common, and No. 2B Common. The...

Simple Logic for Big Problems: An Inside Look at Relational Databases.

ERIC Educational Resources Information Center

Seba, Douglas B.; Smith, Pat

1982-01-01

Discusses database design concept termed "normalization" (process replacing associations between data with associations in two-dimensional tabular form) which results in formation of relational databases (they are to computers what dictionaries are to spoken languages). Applications of the database in serials control and complex systems…

Bifactor model of WISC-IV: Applicability and measurement invariance in low and normal IQ groups.

PubMed

Gomez, Rapson; Vance, Alasdair; Watson, Shaun

2017-07-01

This study examined the applicability and measurement invariance of the bifactor model of the 10 Wechsler Intelligence Scale for Children-Fourth Edition (WISC-IV) core subtests in groups of children and adolescents (age range from 6 to 16 years) with low (IQ ≤79; N = 229; % male = 75.9) and normal (IQ ≥80; N = 816; % male = 75.0) IQ scores. Results supported this model in both groups, and there was good support for measurement invariance for this model across these groups. For all participants together, the omega hierarchical and explained common variance (ECV) values were high for the general factor and low to negligible for the specific factors. Together, the findings favor the use of the Full Scale IQ (FSIQ) scores of the WISC-IV, but not the subscale index scores. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Comparison of normalized gain and Cohen's d for analyzing gains on concept inventories

NASA Astrophysics Data System (ADS)

Nissen, Jayson M.; Talbot, Robert M.; Nasim Thompson, Amreen; Van Dusen, Ben

2018-06-01

Measuring student learning is a complicated but necessary task for understanding the effectiveness of instruction and issues of equity in college science, technology, engineering, and mathematics (STEM) courses. Our investigation focused on the implications on claims about student learning that result from choosing between one of two commonly used metrics for analyzing shifts in concept inventories. The metrics are normalized gain (g ), which is the most common method used in physics education research and other discipline based education research fields, and Cohen's d , which is broadly used in education research and many other fields. Data for the analyses came from the Learning About STEM Student Outcomes (LASSO) database and included test scores from 4551 students on physics, chemistry, biology, and math concept inventories from 89 courses at 17 institutions from across the United States. We compared the two metrics across all the concept inventories. The results showed that the two metrics lead to different inferences about student learning and equity due to the finding that g is biased in favor of high pretest populations. We discuss recommendations for the analysis and reporting of findings on student learning data.

Non-FOOSH Scaphoid Fractures in Young Athletes

PubMed Central

Johnson, Michael R.; Fogarty, Brian T.; Alitz, Curt; Gerber, John P.

2013-01-01

Context: The scaphoid is the most commonly fractured bone in the wrist and can often be difficult to treat and manage, making healing of this fracture problematic. Evidence Acquisition: A search of the entire PubMed (MEDLINE) database using the terms scaphoid fracture management and scaphoid fracture evaluation returned several relevant anatomic and imaging references. Results: Wrist fractures most commonly occur in the scaphoid, which is implicated approximately 60% of the time. The most common mechanism of injury leading to a scaphoid fracture is a fall on an outstretched hand (FOOSH), causing a hyperextension force on the wrist. The following 2 cases, which occurred within 3 months of each other, highlight the difficulty of managing patients with possible scaphoid fractures. Neither patient had a typical FOOSH-related mechanism of injury, and neither was initially tender over the scaphoid. Conclusion: Differential diagnoses should include a scaphoid fracture with any hyperextension traumatic injury (FOOSH or non-FOOSH), even in the absence of scaphoid tenderness and when initial radiographic findings are normal. PMID:24427388

An Approach to Acquiring, Normalizing, and Managing EHR Data From a Clinical Data Repository for Studying Pressure Ulcer Outcomes.

PubMed

Padula, William V; Blackshaw, Leon; Brindle, C Tod; Volchenboum, Samuel L

2016-01-01

Changes in the methods that individual facilities follow to collect and store data related to hospital-acquired pressure ulcer (HAPU) occurrences are essential for improving patient outcomes and advancing our understanding the science behind this clinically relevant issue. Using an established electronic health record system at a large, urban, tertiary-care academic medical center, we investigated the process required for taking raw data of HAPU outcomes and submitting these data to a normalization process. We extracted data from 1.5 million patient shifts and filtered observations to those with a Braden score and linked tables in the electronic health record, including (1) Braden scale scores, (2) laboratory outcomes data, (3) surgical time, (4) provider orders, (5) medications, and (6) discharge diagnoses. Braden scores are important measures specific to HAPUs since these scores clarify the daily risk of a hospitalized patient for developing a pressure ulcer. The other more common measures that may be associated with HAPU outcomes are important to organize in a single data frame with Braden scores according to each patient. Primary keys were assigned to each table, and the data were processed through 3 normalization steps and 1 denormalization step. These processes created 8 tables that can be stored efficiently in a clinical database of HAPU outcomes. As hospitals focus on organizing data for review of HAPUs and other types of hospital-acquired conditions, the normalization process we describe in this article offers directions for collaboration between providers and informatics teams using a common language and structure.

Diabetes mellitus with normal renal function is associated with anaemia.

PubMed

Grossman, Chagai; Dovrish, Zamir; Koren-Morag, Nira; Bornstein, Gil; Leibowitz, Avshalom

2014-05-01

Anaemia is a common complication of diabetes mellitus (DM), usually related to renal failure. There is scarce information as to the levels of haemoglobin (Hb) and the rate of anaemia in diabetic patients with normal renal function. We, therefore, evaluated haemoglobin levels and the rate of anaemia in diabetic subjects with normal renal functions [estimated glomerular filtration rate (eGFR) > 60 mL/min]. The charts of 9250 subjects who attended the Institute of Periodic Medical Examinations at the Chaim Sheba Medical Center for a routine yearly check-up were reviewed. Four hundred and forty-five subjects with type 2 DM and normal renal function were indentified and compared with those without DM who were routinely examined at the same time. Subjects' electronic records were used to build a biochemical and clinical database. Mean haemoglobin levels were lower in subjects with DM than in those without (14.2 vs. 14.7 g/dL, respectively; p < 0.001). Anaemia was observed in 48 (10.8%) subjects in the diabetic group and in only 12 (2.7%) in the nondiabetic group (p < 0.001). Multivariate analysis revealed that age, gender, history of gastrointestinal disease, use of beta blockers, renal function and DM were independent determinants of haemoglobin levels. After adjustment for age, gender, history of gastrointestinal tract diseases and renal function, DM remained a significant determinant of anaemia with an odds ratio of 2.15 (confidence interval: 1.07-4.31). Anaemia is more common in diabetic patients even when eGFR > 60 mL/min. Copyright © 2013 John Wiley & Sons, Ltd.

Comparison of glaucoma diagnostic accuracy of macular ganglion cell complex thickness based on nonhighly myopic and highly myopic normative database

PubMed Central

Chen, Henry Shen-Lih; Liu, Chun-Hsiu; Lu, Da-Wen

2016-01-01

Background/Purpose: To evaluate and compare the diagnostic discriminative ability for detecting glaucoma in highly myopic eyes from a normative database of macular ganglion cell complex (mGCC) thickness based on nonhighly myopic and highly myopic normal eyes. Methods: Forty-nine eyes of 49 participants with high myopia (axial length ≥ 26.0 mm) were enrolled. Spectral-domain optical coherence tomography scans were done using RS-3000, and the mGCC thickness/significance maps within a 9-mm diameter circle were generated using built-in software. We compared the difference of sensitivity, specificity, and diagnostic accuracy between the nonhighly myopic database and the highly myopic database for differentiating the early glaucomatous eyes from the nonglaucomatous eyes. Results: This study enrolled 15 normal eyes and 34 eyes with glaucoma. The mean mGCC thickness of the glaucoma group was significantly less than that of the normal group (p < 0.001). Sensitivity was 96.3%, and the specificity was 50.0% when using the nonhighly myopic normative database. When the highly myopic normative database was used, the sensitivity was 88.9%, and the specificity was 90.0%. The false positive rate was significantly lower when using the highly myopic normative database (p < 0.05). Conclusion: The evaluations of glaucoma in eyes with high myopia using a nonhighly myopic normative database may lead to a frequent misdiagnosis. When evaluating glaucoma in high myopic eyes, the mGCC thickness determined by the long axial length high myopic normative database should be applied. PMID:29018704

Tomato Expression Database (TED): a suite of data presentation and analysis tools

PubMed Central

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150 000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at . PMID:16381976

Tomato Expression Database (TED): a suite of data presentation and analysis tools.

PubMed

Fei, Zhangjun; Tang, Xuemei; Alba, Rob; Giovannoni, James

2006-01-01

The Tomato Expression Database (TED) includes three integrated components. The Tomato Microarray Data Warehouse serves as a central repository for raw gene expression data derived from the public tomato cDNA microarray. In addition to expression data, TED stores experimental design and array information in compliance with the MIAME guidelines and provides web interfaces for researchers to retrieve data for their own analysis and use. The Tomato Microarray Expression Database contains normalized and processed microarray data for ten time points with nine pair-wise comparisons during fruit development and ripening in a normal tomato variety and nearly isogenic single gene mutants impacting fruit development and ripening. Finally, the Tomato Digital Expression Database contains raw and normalized digital expression (EST abundance) data derived from analysis of the complete public tomato EST collection containing >150,000 ESTs derived from 27 different non-normalized EST libraries. This last component also includes tools for the comparison of tomato and Arabidopsis digital expression data. A set of query interfaces and analysis, and visualization tools have been developed and incorporated into TED, which aid users in identifying and deciphering biologically important information from our datasets. TED can be accessed at http://ted.bti.cornell.edu.

Hyperdynamic left ventricular ejection fraction in the intensive care unit.

PubMed

Paonessa, Joseph R; Brennan, Thomas; Pimentel, Marco; Steinhaus, Daniel; Feng, Mengling; Celi, Leo Anthony

2015-08-07

Limited information exists on the etiology, prevalence, and significance of hyperdynamic left ventricular ejection fraction (HDLVEF) in the intensive care unit (ICU). Our aim in the present study was to compare characteristics and outcomes of patients with HDLVEF with those of patients with normal left ventricular ejection fraction in the ICU using a large, public, deidentified critical care database. We conducted a longitudinal, single-center, retrospective cohort study of adult patients who underwent echocardiography during a medical or surgical ICU admission at the Beth Israel Deaconess Medical Center using the Multiparameter Intelligent Monitoring in Intensive Care II database. The final cohort had 2867 patients, of whom 324 had HDLVEF, defined as an ejection fraction >70%. Patients with an ejection fraction <55% were excluded. Compared with critically ill patients with normal left ventricular ejection fraction, the finding of HDLVEF in critically ill patients was associated with female sex, increased age, and the diagnoses of hypertension and cancer. Patients with HDLVEF had increased 28-day mortality compared with those with normal ejection fraction in multivariate logistic regression analysis adjusted for age, sex, Sequential Organ Failure Assessment score, Elixhauser score for comorbidities, vasopressor use, and mechanical ventilation use (odds ratio 1.38, 95% confidence interval 1.039-1.842, p =0.02). The presence of HDLVEF portended increased 28-day mortality, and may be helpful as a gravity marker for prognosis in patients admitted to the ICU. Further research is warranted to gain a better understanding of how these patients respond to common interventions in the ICU and to determine if pharmacologic modulation of HDLVEF improves outcomes.

Assessment of 1H NMR-based metabolomics analysis for normalization of urinary metals against creatinine.

PubMed

Cassiède, Marc; Nair, Sindhu; Dueck, Meghan; Mino, James; McKay, Ryan; Mercier, Pascal; Quémerais, Bernadette; Lacy, Paige

2017-01-01

Proton nuclear magnetic resonance ( 1 H NMR, or NMR) spectroscopy and inductively coupled plasma-mass spectrometry (ICP-MS) are commonly used for metabolomics and metal analysis in urine samples. However, creatinine quantification by NMR for the purpose of normalization of urinary metals has not been validated. We assessed the validity of using NMR analysis for creatinine quantification in human urine samples in order to allow normalization of urinary metal concentrations. NMR and ICP-MS techniques were used to measure metabolite and metal concentrations in urine samples from 10 healthy subjects. For metabolite analysis, two magnetic field strengths (600 and 700MHz) were utilized. In addition, creatinine concentrations were determined by using the Jaffe method. Creatinine levels were strongly correlated (R 2 =0.99) between NMR and Jaffe methods. The NMR spectra were deconvoluted with a target database containing 151 metabolites that are present in urine. A total of 50 metabolites showed good correlation (R 2 =0.7-1.0) at 600 and 700MHz. Metal concentrations determined after NMR-measured creatinine normalization were comparable to previous reports. NMR analysis provided robust urinary creatinine quantification, and was sufficient for normalization of urinary metal concentrations. We found that NMR-measured creatinine-normalized urinary metal concentrations in our control subjects were similar to general population levels in Canada and the United Kingdom. Copyright © 2016 Elsevier B.V. All rights reserved.

Distal Renal Tubular Acidosis and Calcium Nephrolithiasis

NASA Astrophysics Data System (ADS)

Moe, Orson W.; Fuster, Daniel G.; Xie, Xiao-Song

2008-09-01

Calcium stones are commonly encountered in patients with congenital distal renal tubular acidosis, a disease of renal acidification caused by mutations in either the vacuolar H+-ATPase (B1 or a4 subunit), anion exchanger-1, or carbonic anhydrase II. Based on the existing database, we present two hypotheses. First, heterozygotes with mutations in B1 subunit of H+-ATPase are not normal but may harbor biochemical abnormalities such as renal acidification defects, hypercalciuria, and hypocitraturia which can predispose them to kidney stone formation. Second, we propose at least two mechanisms by which mutant B1 subunit can impair H+-ATPase: defective pump assembly and defective pump activity.

An Assessment of Database-Validated microRNA Target Genes in Normal Colonic Mucosa: Implications for Pathway Analysis.

PubMed

Slattery, Martha L; Herrick, Jennifer S; Stevens, John R; Wolff, Roger K; Mullany, Lila E

2017-01-01

Determination of functional pathways regulated by microRNAs (miRNAs), while an essential step in developing therapeutics, is challenging. Some miRNAs have been studied extensively; others have limited information. In this study, we focus on 254 miRNAs previously identified as being associated with colorectal cancer and their database-identified validated target genes. We use RNA-Seq data to evaluate messenger RNA (mRNA) expression for 157 subjects who also had miRNA expression data. In the replication phase of the study, we replicated associations between 254 miRNAs associated with colorectal cancer and mRNA expression of database-identified target genes in normal colonic mucosa. In the discovery phase of the study, we evaluated expression of 18 miR-NAs (those with 20 or fewer database-identified target genes along with miR-21-5p, miR-215-5p, and miR-124-3p which have more than 500 database-identified target genes) with expression of 17 434 mRNAs to identify new targets in colon tissue. Seed region matches between miRNA and newly identified targeted mRNA were used to help determine direct miRNA-mRNA associations. From the replication of the 121 miRNAs that had at least 1 database-identified target gene using mRNA expression methods, 97.9% were expressed in normal colonic mucosa. Of the 8622 target miRNA-mRNA associations identified in the database, 2658 (30.2%) were associated with gene expression in normal colonic mucosa after adjusting for multiple comparisons. Of the 133 miRNAs with database-identified target genes by non-mRNA expression methods, 97.2% were expressed in normal colonic mucosa. After adjustment for multiple comparisons, 2416 miRNA-mRNA associations remained significant (19.8%). Results from the discovery phase based on detailed examination of 18 miRNAs identified more than 80 000 miRNA-mRNA associations that had not previously linked to the miRNA. Of these miRNA-mRNA associations, 15.6% and 14.8% had seed matches for CRCh38 and CRCh37, respectively. Our data suggest that miRNA target gene databases are incomplete; pathways derived from these databases have similar deficiencies. Although we know a lot about several miRNAs, little is known about other miRNAs in terms of their targeted genes. We encourage others to use their data to continue to further identify and validate miRNA-targeted genes.

A kind of improved fingerprinting indoor location method based on WiFi

NASA Astrophysics Data System (ADS)

Zeng, Xi; Lin, Wei

2017-08-01

In the prior inventions, because of the complexity of the indoor environment, it is hard to guarantee position precision. In this paper provides an improved method that can be adopted to increase the indoor positioning accuracy of handheld positioning device. This method will be the direction of the handheld device position Angle and number of access points two characteristics to join the fingerprint. The two parameters make our normal fingerprint database more abundant. The positioning test results from comparing the normal fingerprint database with the improved fingerprint database prove the later positioning more accurate.

Clarifying Normalization

ERIC Educational Resources Information Center

Carpenter, Donald A.

2008-01-01

Confusion exists among database textbooks as to the goal of normalization as well as to which normal form a designer should aspire. This article discusses such discrepancies with the intention of simplifying normalization for both teacher and student. This author's industry and classroom experiences indicate such simplification yields quicker…

PICKLE 2.0: A human protein-protein interaction meta-database employing data integration via genetic information ontology

PubMed Central

Gioutlakis, Aris; Klapa, Maria I.

2017-01-01

It has been acknowledged that source databases recording experimentally supported human protein-protein interactions (PPIs) exhibit limited overlap. Thus, the reconstruction of a comprehensive PPI network requires appropriate integration of multiple heterogeneous primary datasets, presenting the PPIs at various genetic reference levels. Existing PPI meta-databases perform integration via normalization; namely, PPIs are merged after converted to a certain target level. Hence, the node set of the integrated network depends each time on the number and type of the combined datasets. Moreover, the irreversible a priori normalization process hinders the identification of normalization artifacts in the integrated network, which originate from the nonlinearity characterizing the genetic information flow. PICKLE (Protein InteraCtion KnowLedgebasE) 2.0 implements a new architecture for this recently introduced human PPI meta-database. Its main novel feature over the existing meta-databases is its approach to primary PPI dataset integration via genetic information ontology. Building upon the PICKLE principles of using the reviewed human complete proteome (RHCP) of UniProtKB/Swiss-Prot as the reference protein interactor set, and filtering out protein interactions with low probability of being direct based on the available evidence, PICKLE 2.0 first assembles the RHCP genetic information ontology network by connecting the corresponding genes, nucleotide sequences (mRNAs) and proteins (UniProt entries) and then integrates PPI datasets by superimposing them on the ontology network without any a priori transformations. Importantly, this process allows the resulting heterogeneous integrated network to be reversibly normalized to any level of genetic reference without loss of the original information, the latter being used for identification of normalization biases, and enables the appraisal of potential false positive interactions through PPI source database cross-checking. The PICKLE web-based interface (www.pickle.gr) allows for the simultaneous query of multiple entities and provides integrated human PPI networks at either the protein (UniProt) or the gene level, at three PPI filtering modes. PMID:29023571

Construction and comparative evaluation of different activity detection methods in brain FDG-PET.

PubMed

Buchholz, Hans-Georg; Wenzel, Fabian; Gartenschläger, Martin; Thiele, Frank; Young, Stewart; Reuss, Stefan; Schreckenberger, Mathias

2015-08-18

We constructed and evaluated reference brain FDG-PET databases for usage by three software programs (Computer-aided diagnosis for dementia (CAD4D), Statistical Parametric Mapping (SPM) and NEUROSTAT), which allow a user-independent detection of dementia-related hypometabolism in patients' brain FDG-PET. Thirty-seven healthy volunteers were scanned in order to construct brain FDG reference databases, which reflect the normal, age-dependent glucose consumption in human brain, using either software. Databases were compared to each other to assess the impact of different stereotactic normalization algorithms used by either software package. In addition, performance of the new reference databases in the detection of altered glucose consumption in the brains of patients was evaluated by calculating statistical maps of regional hypometabolism in FDG-PET of 20 patients with confirmed Alzheimer's dementia (AD) and of 10 non-AD patients. Extent (hypometabolic volume referred to as cluster size) and magnitude (peak z-score) of detected hypometabolism was statistically analyzed. Differences between the reference databases built by CAD4D, SPM or NEUROSTAT were observed. Due to the different normalization methods, altered spatial FDG patterns were found. When analyzing patient data with the reference databases created using CAD4D, SPM or NEUROSTAT, similar characteristic clusters of hypometabolism in the same brain regions were found in the AD group with either software. However, larger z-scores were observed with CAD4D and NEUROSTAT than those reported by SPM. Better concordance with CAD4D and NEUROSTAT was achieved using the spatially normalized images of SPM and an independent z-score calculation. The three software packages identified the peak z-scores in the same brain region in 11 of 20 AD cases, and there was concordance between CAD4D and SPM in 16 AD subjects. The clinical evaluation of brain FDG-PET of 20 AD patients with either CAD4D-, SPM- or NEUROSTAT-generated databases from an identical reference dataset showed similar patterns of hypometabolism in the brain regions known to be involved in AD. The extent of hypometabolism and peak z-score appeared to be influenced by the calculation method used in each software package rather than by different spatial normalization parameters.

Toward customer-centric organizational science: A common language effect size indicator for multiple linear regressions and regressions with higher-order terms.

PubMed

Krasikova, Dina V; Le, Huy; Bachura, Eric

2018-06-01

To address a long-standing concern regarding a gap between organizational science and practice, scholars called for more intuitive and meaningful ways of communicating research results to users of academic research. In this article, we develop a common language effect size index (CLβ) that can help translate research results to practice. We demonstrate how CLβ can be computed and used to interpret the effects of continuous and categorical predictors in multiple linear regression models. We also elaborate on how the proposed CLβ index is computed and used to interpret interactions and nonlinear effects in regression models. In addition, we test the robustness of the proposed index to violations of normality and provide means for computing standard errors and constructing confidence intervals around its estimates. (PsycINFO Database Record (c) 2018 APA, all rights reserved).

A Comparative Study of Workplace Bullying Among Public and Private Employees in Europe.

PubMed

Ariza-Montes, Antonio; Leal-Rodríguez, Antonio L; Leal-Millán, Antonio G

2015-06-01

Workplace bullying emerges from a set of individual, organizational, and contextual factors. The purpose of this article is hence to identify the influence of these factors among public and private employees. The study is carried out as a statistical-empirical cross-sectional study. The database used was obtained from the 5th European Working Conditions Survey 2010. The results reveal a common core with respect to the factors that determine workplace bullying. Despite this common base that integrates both models, the distinctive features of the harassed employee within the public sector deal with age, full-time work, the greater nighttime associated with certain public service professions, and a lower level of motivation. The present work summarizes a set of implications and proposes that, under normal conditions, workplace bullying could be reduced if job demands are limited and job resources are increased.

OrganismTagger: detection, normalization and grounding of organism entities in biomedical documents.

PubMed

Naderi, Nona; Kappler, Thomas; Baker, Christopher J O; Witte, René

2011-10-01

Semantic tagging of organism mentions in full-text articles is an important part of literature mining and semantic enrichment solutions. Tagged organism mentions also play a pivotal role in disambiguating other entities in a text, such as proteins. A high-precision organism tagging system must be able to detect the numerous forms of organism mentions, including common names as well as the traditional taxonomic groups: genus, species and strains. In addition, such a system must resolve abbreviations and acronyms, assign the scientific name and if possible link the detected mention to the NCBI Taxonomy database for further semantic queries and literature navigation. We present the OrganismTagger, a hybrid rule-based/machine learning system to extract organism mentions from the literature. It includes tools for automatically generating lexical and ontological resources from a copy of the NCBI Taxonomy database, thereby facilitating system updates by end users. Its novel ontology-based resources can also be reused in other semantic mining and linked data tasks. Each detected organism mention is normalized to a canonical name through the resolution of acronyms and abbreviations and subsequently grounded with an NCBI Taxonomy database ID. In particular, our system combines a novel machine-learning approach with rule-based and lexical methods for detecting strain mentions in documents. On our manually annotated OT corpus, the OrganismTagger achieves a precision of 95%, a recall of 94% and a grounding accuracy of 97.5%. On the manually annotated corpus of Linnaeus-100, the results show a precision of 99%, recall of 97% and grounding accuracy of 97.4%. The OrganismTagger, including supporting tools, resources, training data and manual annotations, as well as end user and developer documentation, is freely available under an open-source license at http://www.semanticsoftware.info/organism-tagger. witte@semanticsoftware.info.

An informatics approach to integrating genetic and neurological data in speech and language neuroscience.

PubMed

Bohland, Jason W; Myers, Emma M; Kim, Esther

2014-01-01

A number of heritable disorders impair the normal development of speech and language processes and occur in large numbers within the general population. While candidate genes and loci have been identified, the gap between genotype and phenotype is vast, limiting current understanding of the biology of normal and disordered processes. This gap exists not only in our scientific knowledge, but also in our research communities, where genetics researchers and speech, language, and cognitive scientists tend to operate independently. Here we describe a web-based, domain-specific, curated database that represents information about genotype-phenotype relations specific to speech and language disorders, as well as neuroimaging results demonstrating focal brain differences in relevant patients versus controls. Bringing these two distinct data types into a common database ( http://neurospeech.org/sldb ) is a first step toward bringing molecular level information into cognitive and computational theories of speech and language function. One bridge between these data types is provided by densely sampled profiles of gene expression in the brain, such as those provided by the Allen Brain Atlases. Here we present results from exploratory analyses of human brain gene expression profiles for genes implicated in speech and language disorders, which are annotated in our database. We then discuss how such datasets can be useful in the development of computational models that bridge levels of analysis, necessary to provide a mechanistic understanding of heritable language disorders. We further describe our general approach to information integration, discuss important caveats and considerations, and offer a specific but speculative example based on genes implicated in stuttering and basal ganglia function in speech motor control.

Relational Database Design in Information Science Education.

ERIC Educational Resources Information Center

Brooks, Terrence A.

1985-01-01

Reports on database management system (dbms) applications designed by library school students for university community at University of Iowa. Three dbms design issues are examined: synthesis of relations, analysis of relations (normalization procedure), and data dictionary usage. Database planning prior to automation using data dictionary approach…

Results of Database Studies in Spine Surgery Can Be Influenced by Missing Data.

PubMed

Basques, Bryce A; McLynn, Ryan P; Fice, Michael P; Samuel, Andre M; Lukasiewicz, Adam M; Bohl, Daniel D; Ahn, Junyoung; Singh, Kern; Grauer, Jonathan N

2017-12-01

National databases are increasingly being used for research in spine surgery; however, one limitation of such databases that has received sparse mention is the frequency of missing data. Studies using these databases often do not emphasize the percentage of missing data for each variable used and do not specify how patients with missing data are incorporated into analyses. This study uses the American College of Surgeons National Surgical Quality Improvement Program (ACS-NSQIP) database to examine whether different treatments of missing data can influence the results of spine studies. (1) What is the frequency of missing data fields for demographics, medical comorbidities, preoperative laboratory values, operating room times, and length of stay recorded in ACS-NSQIP? (2) Using three common approaches to handling missing data, how frequently do those approaches agree in terms of finding particular variables to be associated with adverse events? (3) Do different approaches to handling missing data influence the outcomes and effect sizes of an analysis testing for an association with these variables with occurrence of adverse events? Patients who underwent spine surgery between 2005 and 2013 were identified from the ACS-NSQIP database. A total of 88,471 patients undergoing spine surgery were identified. The most common procedures were anterior cervical discectomy and fusion, lumbar decompression, and lumbar fusion. Demographics, comorbidities, and perioperative laboratory values were tabulated for each patient, and the percent of missing data was noted for each variable. These variables were tested for an association with "any adverse event" using three separate multivariate regressions that used the most common treatments for missing data. In the first regression, patients with any missing data were excluded. In the second regression, missing data were treated as a negative or "reference" value; for continuous variables, the mean of each variable's reference range was computed and imputed. In the third regression, any variables with > 10% rate of missing data were removed from the regression; among variables with ≤ 10% missing data, individual cases with missing values were excluded. The results of these regressions were compared to determine how the different treatments of missing data could affect the results of spine studies using the ACS-NSQIP database. Of the 88,471 patients, as many as 4441 (5%) had missing elements among demographic data, 69,184 (72%) among comorbidities, 70,892 (80%) among preoperative laboratory values, and 56,551 (64%) among operating room times. Considering the three different treatments of missing data, we found different risk factors for adverse events. Of 44 risk factors found to be associated with adverse events in any analysis, only 15 (34%) of these risk factors were common among the three regressions. The second treatment of missing data (assuming "normal" value) found the most risk factors (40) to be associated with any adverse event, whereas the first treatment (deleting patients with missing data) found the fewest associations at 20. Among the risk factors associated with any adverse event, the 10 with the greatest effect size (odds ratio) by each regression were ranked. Of the 15 variables in the top 10 for any regression, six of these were common among all three lists. Differing treatments of missing data can influence the results of spine studies using the ACS-NSQIP. The current study highlights the importance of considering how such missing data are handled. Until there are better guidelines on the best approaches to handle missing data, investigators should report how missing data were handled to increase the quality and transparency of orthopaedic database research. Readers of large database studies should note whether handling of missing data was addressed and consider potential bias with high rates or unspecified or weak methods for handling missing data.

Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods.

PubMed

Wang, Liming; Zhu, L; Luan, R; Wang, L; Fu, J; Wang, X; Sui, L

2016-10-10

Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT) were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family). Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1), potential TFs, as well as potential miRNAs, might be involved in DCM.

Analyzing gene expression profiles in dilated cardiomyopathy via bioinformatics methods

PubMed Central

Wang, Liming; Zhu, L.; Luan, R.; Wang, L.; Fu, J.; Wang, X.; Sui, L.

2016-01-01

Dilated cardiomyopathy (DCM) is characterized by ventricular dilatation, and it is a common cause of heart failure and cardiac transplantation. This study aimed to explore potential DCM-related genes and their underlying regulatory mechanism using methods of bioinformatics. The gene expression profiles of GSE3586 were downloaded from Gene Expression Omnibus database, including 15 normal samples and 13 DCM samples. The differentially expressed genes (DEGs) were identified between normal and DCM samples using Limma package in R language. Pathway enrichment analysis of DEGs was then performed. Meanwhile, the potential transcription factors (TFs) and microRNAs (miRNAs) of these DEGs were predicted based on their binding sequences. In addition, DEGs were mapped to the cMap database to find the potential small molecule drugs. A total of 4777 genes were identified as DEGs by comparing gene expression profiles between DCM and control samples. DEGs were significantly enriched in 26 pathways, such as lymphocyte TarBase pathway and androgen receptor signaling pathway. Furthermore, potential TFs (SP1, LEF1, and NFAT) were identified, as well as potential miRNAs (miR-9, miR-200 family, and miR-30 family). Additionally, small molecules like isoflupredone and trihexyphenidyl were found to be potential therapeutic drugs for DCM. The identified DEGs (PRSS12 and FOXG1), potential TFs, as well as potential miRNAs, might be involved in DCM. PMID:27737314

An overview of systematic reviews of normal labor and delivery management

PubMed Central

Iravani, Mina; Janghorbani, Mohsen; Zarean, Elahe; Bahrami, Masoud

2015-01-01

Background: Despite the scientific and medical advances for management of complicated health issues, the current maternity care setting has increased risks for healthy women and their babies. The aim of this study was to conduct an overview of published systematic reviews on the interventions used most commonly for management of normal labor and delivery in the first stage of labor. Materials and Methods: The online databases through March 2013, limited to systematic reviews of clinical trials were searched. An updated search was performed in April 2014. Two reviewers independently assessed data inclusion, extraction, and quality of methodology. Results: Twenty-three reviews (16 Cochrane, 7 non-Cochrane), relating to the most common care practices for management of normal labor and delivery in the first stage of labor, were included. Evidence does not support routine enemas, routine perineal shaving, continuous electronic fetal heart rate monitoring, routine early amniotomy, and restriction of fluids and food during labor. Evidence supports continuity of midwifery care and support, encouragement to non-supine position, and freedom in movement throughout labor. There is insufficient evidence to support routine administration of intravenous fluids and antispasmodics during labor. More evidence is needed regarding delayed admission until active labor and use of partograph. Conclusions: Evidence-based maternity care emphasizes on the practices that increase safety for mother and baby. If policymakers and healthcare providers wish to promote obstetric care quality successfully, it is important that they implement evidence-based clinical practices in routine midwifery care. PMID:26120327

An overview of systematic reviews of normal labor and delivery management.

PubMed

Iravani, Mina; Janghorbani, Mohsen; Zarean, Elahe; Bahrami, Masoud

2015-01-01

Despite the scientific and medical advances for management of complicated health issues, the current maternity care setting has increased risks for healthy women and their babies. The aim of this study was to conduct an overview of published systematic reviews on the interventions used most commonly for management of normal labor and delivery in the first stage of labor. The online databases through March 2013, limited to systematic reviews of clinical trials were searched. An updated search was performed in April 2014. Two reviewers independently assessed data inclusion, extraction, and quality of methodology. Twenty-three reviews (16 Cochrane, 7 non-Cochrane), relating to the most common care practices for management of normal labor and delivery in the first stage of labor, were included. Evidence does not support routine enemas, routine perineal shaving, continuous electronic fetal heart rate monitoring, routine early amniotomy, and restriction of fluids and food during labor. Evidence supports continuity of midwifery care and support, encouragement to non-supine position, and freedom in movement throughout labor. There is insufficient evidence to support routine administration of intravenous fluids and antispasmodics during labor. More evidence is needed regarding delayed admission until active labor and use of partograph. Evidence-based maternity care emphasizes on the practices that increase safety for mother and baby. If policymakers and healthcare providers wish to promote obstetric care quality successfully, it is important that they implement evidence-based clinical practices in routine midwifery care.

[Characteristics of acupoint application for the sub-healthy condition treated with ancient and modern acupuncture based on data mining exploration].

PubMed

Cai, Liyan; Wu, Jie; Ma, Tingting; Yang, Lijie

2015-10-01

The acupoint selection was retrieved from the ancient and modern literature on the treatment of sub-healthy condition with acupuncture. The law of acupoint application was analyzed so as to provide a certain reference to the determination of acupoint prescription in clinical acupuncture. The ancient literature was retrieved from Chinese basic ancient literature database. The modern literature was retrieved from Cochrane Library, Medline, PubMed, Ovid evidence-based medicine database, Chinese biomedical literature database, China journal full-text database, VIP journal full-text database and Wanfang database. The database mining software was adopted to explore the law of acupoint application in treatment of sub-healthy conditions with ancient and modern acupuncture. The acupoint use frequency, compatibility association rule, law for meridian use and the use regularity of specific points were analyzed. In the ancient treatment for sub-healthy condition, the top five commonly used acupoints are Shenmen (HT 7), Zhaohai (KI 6), Taibai (SP 3), Daling (PC 7) and Taixi (KI 3). The most commonly combined points are Zhangmen (LR 13), Taibai (SP 3) and Zhaohai (KI 6). The most commonly used meridians are the bladder meridian of foot-taiyang, kidney meridian of foot-shaoyin and liver meridian of foot-jueyin. The most commonly used specific points are the five-shu points. The most commonly used acupoints are located in the lower limbs. In the modern treatment, the top five commonly used acupoints are Zusanli (ST 36), Sanyinjiao (SP 6), Baihui (GV 20), Shenshu (BL 23) and Guanyuan (CV 4). The most commonly supplemented points are Hegu (LI 4) and Taichong (LR 3). The most commonly used meridians are the bladder meridian of foot-taiyang, the conception vessel and the governor vessel. The most commonly used specific points are the back-shu points. The most commonly used acupoints are located in the lower limbs. After the systematic comprehension of the relevant ancient and modern literature, the most commonly used acupoints are selected along the bladder meridian of foot-taiyang, and the most commonly used specific points are the back-shu points, the five-shu points and the front-mu-points. the acupoints are mostly located in the lower limbs.

The Eruption Forecasting Information System (EFIS) database project

NASA Astrophysics Data System (ADS)

Ogburn, Sarah; Harpel, Chris; Pesicek, Jeremy; Wellik, Jay; Pallister, John; Wright, Heather

2016-04-01

The Eruption Forecasting Information System (EFIS) project is a new initiative of the U.S. Geological Survey-USAID Volcano Disaster Assistance Program (VDAP) with the goal of enhancing VDAP's ability to forecast the outcome of volcanic unrest. The EFIS project seeks to: (1) Move away from relying on the collective memory to probability estimation using databases (2) Create databases useful for pattern recognition and for answering common VDAP questions; e.g. how commonly does unrest lead to eruption? how commonly do phreatic eruptions portend magmatic eruptions and what is the range of antecedence times? (3) Create generic probabilistic event trees using global data for different volcano 'types' (4) Create background, volcano-specific, probabilistic event trees for frequently active or particularly hazardous volcanoes in advance of a crisis (5) Quantify and communicate uncertainty in probabilities A major component of the project is the global EFIS relational database, which contains multiple modules designed to aid in the construction of probabilistic event trees and to answer common questions that arise during volcanic crises. The primary module contains chronologies of volcanic unrest, including the timing of phreatic eruptions, column heights, eruptive products, etc. and will be initially populated using chronicles of eruptive activity from Alaskan volcanic eruptions in the GeoDIVA database (Cameron et al. 2013). This database module allows us to query across other global databases such as the WOVOdat database of monitoring data and the Smithsonian Institution's Global Volcanism Program (GVP) database of eruptive histories and volcano information. The EFIS database is in the early stages of development and population; thus, this contribution also serves as a request for feedback from the community.

Deriving leaf mass per area (LMA) from foliar reflectance across a variety of plant species using continuous wavelet analysis

NASA Astrophysics Data System (ADS)

Cheng, Tao; Rivard, Benoit; Sánchez-Azofeifa, Arturo G.; Féret, Jean-Baptiste; Jacquemoud, Stéphane; Ustin, Susan L.

2014-01-01

Leaf mass per area (LMA), the ratio of leaf dry mass to leaf area, is a trait of central importance to the understanding of plant light capture and carbon gain. It can be estimated from leaf reflectance spectroscopy in the infrared region, by making use of information about the absorption features of dry matter. This study reports on the application of continuous wavelet analysis (CWA) to the estimation of LMA across a wide range of plant species. We compiled a large database of leaf reflectance spectra acquired within the framework of three independent measurement campaigns (ANGERS, LOPEX and PANAMA) and generated a simulated database using the PROSPECT leaf optical properties model. CWA was applied to the measured and simulated databases to extract wavelet features that correlate with LMA. These features were assessed in terms of predictive capability and robustness while transferring predictive models from the simulated database to the measured database. The assessment was also conducted with two existing spectral indices, namely the Normalized Dry Matter Index (NDMI) and the Normalized Difference index for LMA (NDLMA). Five common wavelet features were determined from the two databases, which showed significant correlations with LMA (R2: 0.51-0.82, p < 0.0001). The best robustness (R2 = 0.74, RMSE = 18.97 g/m2 and Bias = 0.12 g/m2) was obtained using a combination of two low-scale features (1639 nm, scale 4) and (2133 nm, scale 5), the first being predominantly important. The transferability of the wavelet-based predictive model to the whole measured database was either better than or comparable to those based on spectral indices. Additionally, only the wavelet-based model showed consistent predictive capabilities among the three measured data sets. In comparison, the models based on spectral indices were sensitive to site-specific data sets. Integrating the NDLMA spectral index and the two robust wavelet features improved the LMA prediction. One of the bands used by this spectral index, 1368 nm, was located in a strong atmospheric water absorption region and replacing it with the next available band (1340 nm) led to lower predictive accuracies. However, the two wavelet features were not affected by data quality in the atmospheric absorption regions and therefore showed potential for canopy-level investigations. The wavelet approach provides a different perspective into spectral responses to LMA variation than the traditional spectral indices and holds greater promise for implementation with airborne or spaceborne imaging spectroscopy data for mapping canopy foliar dry biomass.

Wind turbine reliability database update.

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

Peters, Valerie A.; Hill, Roger Ray; Stinebaugh, Jennifer A.

2009-03-01

This report documents the status of the Sandia National Laboratories' Wind Plant Reliability Database. Included in this report are updates on the form and contents of the Database, which stems from a fivestep process of data partnerships, data definition and transfer, data formatting and normalization, analysis, and reporting. Selected observations are also reported.

Presenting phenotype of paediatric inflammatory bowel disease in Wessex, Southern England 2010-2013.

PubMed

Ashton, J J; Coelho, T; Ennis, S; Batra, A; Afzal, N A; Beattie, R M

2015-08-01

There has been at least a twofold increase in the incidence of paediatric inflammatory bowel disease (PIBD) over the last 20 years; we report the presenting features from 2010 to 2013 and compare with previous data. All patients diagnosed with PIBD at University Hospitals Southampton from 2010 to 2013 were identified from an in-house database. Data were obtained from paper and electronic notes. Height, weight and BMI SDS are presented as median values (95% CI). One hundred and seventy-two patients were included (median age at diagnosis 13.5, 115 male); Crohn's disease (CD) - 107, UC - 50, inflammatory bowel disease unclassified (IBDU) - 15. The most common presenting features of CD were abdominal pain (86%), diarrhoea (78.5%) and weight loss (56.1%); 42.1% of patients had all three. In UC blood in stool (92%), diarrhoea (92%) and abdominal pain (88%) were the most common; all three in 76% of patients. CD presented with ileocolonic disease in 52.5%. UC presented with pancolitis in 64%. There was growth delay in CD: height -0.37 (-0.60 to -0.14); weight -1.09 (-1.35 to -0.83). Growth was maintained in UC: height 0.53 (0.19 to 0.87); weight 0.14 (-0.20 to 0.48). Paediatric inflammatory bowel disease phenotype remains as extensive despite increasing incidence. Although the classical phenotype is common, a reasonable proportion present with atypical features, normal growth and normal blood markers. ©2015 Foundation Acta Paediatrica. Published by John Wiley & Sons Ltd.

Parenting and later substance use among Mexican-origin youth: Moderation by preference for a common language.

PubMed

Schofield, Thomas J; Toro, Rosa I; Parke, Ross D; Cookston, Jeffrey T; Fabricius, William V; Coltrane, Scott

2017-04-01

The primary goal of the current study was to test whether parent and adolescent preference for a common language moderates the association between parenting and rank-order change over time in offspring substance use. A sample of Mexican-origin 7th-grade adolescents (Mage = 12.5 years, N = 194, 52% female) was measured longitudinally on use of tobacco, alcohol, and marijuana. Mothers, fathers, and adolescents all reported on consistent discipline and monitoring of adolescents. Both consistent discipline and monitoring predicted relative decreases in substance use into early adulthood but only among parent-offspring dyads who expressed preference for the same language (either English or Spanish). This moderation held after controlling for parent substance use, family structure, having completed schooling in Mexico, years lived in the United States, family income, and cultural values. An unintended consequence of the immigration process may be the loss of parenting effectiveness that is normally present when parents and adolescents prefer to communicate in a common language. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

[Dangerous cosmetic products in Germany : Analysis of the RAPEX database of the European Commission].

PubMed

Elsner, P; Schliemann, S

2017-11-01

Cosmetic products are subject to the European Cosmetics Regulation: They shall not harm human health when used under "normal or reasonably foreseeable conditions". Hazardous cosmetic products are reported by the EU Member States to the EU Commission and are listed in the database of the European Rapid Alert System RAPEX. The reports from Germany on dangerous cosmetic products from the years 2005-3/2017 in the European RAPEX database were systematically analyzed. During the study period, 157 dangerous cosmetic products were reported from Germany. The most common product categories were bleaching creams (24.2%) because of the content of hydroquinone, mercury or corticosteroids, creams/lotions/gels (10.8%) mainly due to microbiological contamination, henna products (10.2%) because of sensitizing concentrations of paraphenylene diamine, and nail adhesives (8.9%) because of high levels of methyl methacrylate. Hazardous cosmetic products appear to be rare in view of the high market volume of cosmetics, even though the total number of official investigations the RAPEX reports based on is not known. Dermatologists should inform the competent monitoring authorities in case of a suspected harm to health caused by dangerous cosmetic products so that the products can be examined and, if necessary, withdrawn from the market.

FunShift: a database of function shift analysis on protein subfamilies

PubMed Central

Abhiman, Saraswathi; Sonnhammer, Erik L. L.

2005-01-01

Members of a protein family normally have a general biochemical function in common, but frequently one or more subgroups have evolved a slightly different function, such as different substrate specificity. It is important to detect such function shifts for a more accurate functional annotation. The FunShift database described here is a compilation of function shift analysis performed between subfamilies in protein families. It consists of two main components: (i) subfamilies derived from protein domain families and (ii) pairwise subfamily comparisons analyzed for function shift. The present release, FunShift 12, was derived from Pfam 12 and consists of 151 934 subfamilies derived from 7300 families. We carried out function shift analysis by two complementary methods on families with up to 500 members. From a total of 179 210 subfamily pairs, 62 384 were predicted to be functionally shifted in 2881 families. Each subfamily pair is provided with a markup of probable functional specificity-determining sites. Tools for searching and exploring the data are provided to make this database a valuable resource for protein function annotation. Knowledge of these functionally important sites will be useful for experimental biologists performing functional mutation studies. FunShift is available at http://FunShift.cgb.ki.se. PMID:15608176

Methods and means used in programming intelligent searches of technical documents

NASA Technical Reports Server (NTRS)

Gross, David L.

1993-01-01

In order to meet the data research requirements of the Safety, Reliability & Quality Assurance activities at Kennedy Space Center (KSC), a new computer search method for technical data documents was developed. By their very nature, technical documents are partially encrypted because of the author's use of acronyms, abbreviations, and shortcut notations. This problem of computerized searching is compounded at KSC by the volume of documentation that is produced during normal Space Shuttle operations. The Centralized Document Database (CDD) is designed to solve this problem. It provides a common interface to an unlimited number of files of various sizes, with the capability to perform any diversified types and levels of data searches. The heart of the CDD is the nature and capability of its search algorithms. The most complex form of search that the program uses is with the use of a domain-specific database of acronyms, abbreviations, synonyms, and word frequency tables. This database, along with basic sentence parsing, is used to convert a request for information into a relational network. This network is used as a filter on the original document file to determine the most likely locations for the data requested. This type of search will locate information that traditional techniques, (i.e., Boolean structured key-word searching), would not find.

Osteoporosis diagnosis in men: the T-score controversy revisited.

PubMed

Binkley, Neil; Adler, Robert; Bilezikian, John P

2014-12-01

Osteoporosis becomes common with aging in both sexes, but is often ignored in men. The 2013 International Society for Clinical Densitometry consensus conference endorsed a Caucasian female referent database for T-score calculation in men. This recommendation has generated controversy and concern. Accumulating data indicate that at the same DXA-measured body mineral density (BMD) (g/cm(2)), men and women are at approximately the same fracture risk. With this point in mind, using the same database to derive the T-score in men and women is reasonable. As a result, a greater proportion of men who sustain a fragility fracture will have T-scores that are higher than they would if a male database were used; in fact, many men will fracture at T-scores that are "normal." This highlights the importance of diagnosing osteoporosis not just by T-score, but also by the presence of fragility fracture and/or by estimations of fracture risk as generated by tools such as the FRAX calculator. The practical consequences of this change in densitometric definition of osteoporosis in men should be monitored, including the proportion of men at risk identified and treated as well as defining the response to treatment in those assessed by this more comprehensive approach.

Identification of osteosarcoma-related specific proteins in serum samples using surface-enhanced laser desorption/ionization-time-of-flight mass spectrometry.

PubMed

Gu, Jianli; Li, Jitian; Huang, Manyu; Zhang, Zhiyong; Li, Dongsheng; Song, Guoying; Ding, Xingpo; Li, Wuyin

2014-01-01

Osteosarcoma (OS) is the most common malignant bone tumor. To identify OS-related specific proteins for early diagnosis of OS, a novel approach, surface-enhanced laser desorption/ionization-time-of-flight mass spectrometry (SELDI-TOF-MS) to serum samples from 25 OS patients, 16 osteochondroma, and 26 age-matched normal human volunteers as controls, was performed. Two proteins showed a significantly different expression in OS serum samples from control groups. Proteomic profiles and external leave-one-out cross-validation analysis showed that the correct rate of allocation, the sensitivity, and the specificity of diagnosis were 100%. These two proteins were further identified by searching the EPO-KB database, and one of the proteins identified as Serine rich region profile is involved in various cellular signaling cascades and tumor genesis. The presence of these two proteins in OS patients but absence from premalignant and normal human controls implied that they can be potential biomarkers for early diagnosis of OS.

Sulfur Mustard Effects on Mental Health and Quality-of-Life: A Review.

PubMed

Razavi, Seyed Mansour; Negahban, Zahra; Pirhosseinloo, Mohsen; Razavi, Mahdiyeh Sadat; Hadjati, Gholamreza; Salamati, Payman

2014-01-01

Mental disorders are more common among the chemically injured veterans rather the than the normal population. The main aim of this study was to evaluate the effects of mustard gas (MG) on mental health and quality-of-life (QOL) in the people exposed to it based on reviewing valid published articles. We searched English databases including Medline, ISI and Scopus as well as Farsi databases including Iranmedex and Irandoc and reviewed them. The used keywords were in two English and Farsi languages. Forty related full texts out of more than 300 articles were assessed and for their qualification, only the publications in accredited journals were considered sufficient. The average mental health score of victims using the general health questionnaire (GHQ) was 48.92. The frequency of anxiety was (18-65%), insomnia (13.63%), social performance disturbances (10.73%), severe depression (6-46%), low concentration (54%), emotional problems (98%), behavioral abnormalities (80%), thought processing disturbances (14%), memory impairment (80%), personality disorders (31%), seizures (6%), psychosis (3%). Post-traumatic stress disorder (PTSD) is one of the most common and important disorders with lifetime PTSD (8-59%), current PTSD (2-33%) and the QOL in chemical warfare victims decreased. Exposure to chemical weapons may lead to physical, mental, social, and economic damages and consequently decrease the victims' (QOL. Therefore, they should be taken into more care.

Sulfur Mustard Effects on Mental Health and Quality-of-Life: A Review

PubMed Central

Razavi, Seyed Mansour; Negahban, Zahra; Pirhosseinloo, Mohsen; Razavi, Mahdiyeh Sadat; Hadjati, Gholamreza; Salamati, Payman

2014-01-01

Objective: Mental disorders are more common among the chemically injured veterans rather the than the normal population. The main aim of this study was to evaluate the effects of mustard gas (MG) on mental health and quality-of-life (QOL) in the people exposed to it based on reviewing valid published articles. Methods: We searched English databases including Medline, ISI and Scopus as well as Farsi databases including Iranmedex and Irandoc and reviewed them. The used keywords were in two English and Farsi languages. Forty related full texts out of more than 300 articles were assessed and for their qualification, only the publications in accredited journals were considered sufficient. Results: The average mental health score of victims using the general health questionnaire (GHQ) was 48.92. The frequency of anxiety was (18-65%), insomnia (13.63%), social performance disturbances (10.73%), severe depression (6-46%), low concentration (54%), emotional problems (98%), behavioral abnormalities (80%), thought processing disturbances (14%), memory impairment (80%), personality disorders (31%), seizures (6%), psychosis (3%). Post-traumatic stress disorder (PTSD) is one of the most common and important disorders with lifetime PTSD (8-59%), current PTSD (2-33%) and the QOL in chemical warfare victims decreased. Conclusion: Exposure to chemical weapons may lead to physical, mental, social, and economic damages and consequently decrease the victims’ (QOL. Therefore, they should be taken into more care. PMID:25780370

Graph Databases for Large-Scale Healthcare Systems: A Framework for Efficient Data Management and Data Services

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

Park, Yubin; Shankar, Mallikarjun; Park, Byung H.

Designing a database system for both efficient data management and data services has been one of the enduring challenges in the healthcare domain. In many healthcare systems, data services and data management are often viewed as two orthogonal tasks; data services refer to retrieval and analytic queries such as search, joins, statistical data extraction, and simple data mining algorithms, while data management refers to building error-tolerant and non-redundant database systems. The gap between service and management has resulted in rigid database systems and schemas that do not support effective analytics. We compose a rich graph structure from an abstracted healthcaremore » RDBMS to illustrate how we can fill this gap in practice. We show how a healthcare graph can be automatically constructed from a normalized relational database using the proposed 3NF Equivalent Graph (3EG) transformation.We discuss a set of real world graph queries such as finding self-referrals, shared providers, and collaborative filtering, and evaluate their performance over a relational database and its 3EG-transformed graph. Experimental results show that the graph representation serves as multiple de-normalized tables, thus reducing complexity in a database and enhancing data accessibility of users. Based on this finding, we propose an ensemble framework of databases for healthcare applications.« less

Aptamer Database

PubMed Central

Lee, Jennifer F.; Hesselberth, Jay R.; Meyers, Lauren Ancel; Ellington, Andrew D.

2004-01-01

The aptamer database is designed to contain comprehensive sequence information on aptamers and unnatural ribozymes that have been generated by in vitro selection methods. Such data are not normally collected in ‘natural’ sequence databases, such as GenBank. Besides serving as a storehouse of sequences that may have diagnostic or therapeutic utility, the database serves as a valuable resource for theoretical biologists who describe and explore fitness landscapes. The database is updated monthly and is publicly available at http://aptamer.icmb.utexas.edu/. PMID:14681367

TAP score: torsion angle propensity normalization applied to local protein structure evaluation

PubMed Central

Tosatto, Silvio CE; Battistutta, Roberto

2007-01-01

Background Experimentally determined protein structures may contain errors and require validation. Conformational criteria based on the Ramachandran plot are mainly used to distinguish between distorted and adequately refined models. While the readily available criteria are sufficient to detect totally wrong structures, establishing the more subtle differences between plausible structures remains more challenging. Results A new criterion, called TAP score, measuring local sequence to structure fitness based on torsion angle propensities normalized against the global minimum and maximum is introduced. It is shown to be more accurate than previous methods at estimating the validity of a protein model in terms of commonly used experimental quality parameters on two test sets representing the full PDB database and a subset of obsolete PDB structures. Highly selective TAP thresholds are derived to recognize over 90% of the top experimental structures in the absence of experimental information. Both a web server and an executable version of the TAP score are available at . Conclusion A novel procedure for energy normalization (TAP) has significantly improved the possibility to recognize the best experimental structures. It will allow the user to more reliably isolate problematic structures in the context of automated experimental structure determination. PMID:17504537

Teaching Case: Adapting the Access Northwind Database to Support a Database Course

ERIC Educational Resources Information Center

Dyer, John N.; Rogers, Camille

2015-01-01

A common problem encountered when teaching database courses is that few large illustrative databases exist to support teaching and learning. Most database textbooks have small "toy" databases that are chapter objective specific, and thus do not support application over the complete domain of design, implementation and management concepts…

Repetitive Bibliographical Information in Relational Databases.

ERIC Educational Resources Information Center

Brooks, Terrence A.

1988-01-01

Proposes a solution to the problem of loading repetitive bibliographic information in a microcomputer-based relational database management system. The alternative design described is based on a representational redundancy design and normalization theory. (12 references) (Author/CLB)

Impact of renal dysfunction on outcomes of coronary artery bypass surgery: results from the Society of Thoracic Surgeons National Adult Cardiac Database.

PubMed

Cooper, William A; O'Brien, Sean M; Thourani, Vinod H; Guyton, Robert A; Bridges, Charles R; Szczech, Lynda A; Petersen, Rebecca; Peterson, Eric D

2006-02-28

Although patients with end-stage renal disease are known to be at high risk for mortality after coronary artery bypass graft (CABG) surgery, the impact of lesser degrees of renal impairment has not been well studied. The purpose of this study was to compare outcomes in patients undergoing CABG with a range from normal renal function to dependence on dialysis. We reviewed 483,914 patients receiving isolated CABG from July 2000 to December 2003, using the Society of Thoracic Surgeons National Adult Cardiac Database. Glomerular filtration rate (GFR) was estimated for patients with the use of the Modification of Diet in Renal Disease study formula. Multivariable logistic regression was used to determine the association of GFR with operative mortality and morbidities (stroke, reoperation, deep sternal infection, ventilation >48 hours, postoperative stay >2 weeks) after adjustment for 27 other known clinical risk factors. Preoperative renal dysfunction (RD) was common among CABG patients, with 51% having mild RD (GFR 60 to 90 mL/min per 1.73 m2, excludes dialysis), 24% moderate RD (GFR 30 to 59 mL/min per 1.73 m2, excludes dialysis), 2% severe RD (GFR <30 mL/min per 1.73 m2, excludes dialysis), and 1.5% requiring dialysis. Operative mortality rose inversely with declining renal function, from 1.3% for those with normal renal function to 9.3% for patients with severe RD not on dialysis and 9.0% for those who were dialysis dependent. After adjustment for other covariates, preoperative GFR was one of the most powerful predictors of operative mortality and morbidities. Preoperative RD is common in the CABG population and carries important prognostic importance. Assessment of preoperative renal function should be incorporated into clinical risk assessment and prediction models.

Applications of Database Machines in Library Systems.

ERIC Educational Resources Information Center

Salmon, Stephen R.

1984-01-01

Characteristics and advantages of database machines are summarized and their applications to library functions are described. The ability to attach multiple hosts to the same database and flexibility in choosing operating and database management systems for different functions without loss of access to common database are noted. (EJS)

Using a Semi-Realistic Database to Support a Database Course

ERIC Educational Resources Information Center

Yue, Kwok-Bun

2013-01-01

A common problem for university relational database courses is to construct effective databases for instructions and assignments. Highly simplified "toy" databases are easily available for teaching, learning, and practicing. However, they do not reflect the complexity and practical considerations that students encounter in real-world…

A high-performance spatial database based approach for pathology imaging algorithm evaluation

PubMed Central

Wang, Fusheng; Kong, Jun; Gao, Jingjing; Cooper, Lee A.D.; Kurc, Tahsin; Zhou, Zhengwen; Adler, David; Vergara-Niedermayr, Cristobal; Katigbak, Bryan; Brat, Daniel J.; Saltz, Joel H.

2013-01-01

Background: Algorithm evaluation provides a means to characterize variability across image analysis algorithms, validate algorithms by comparison with human annotations, combine results from multiple algorithms for performance improvement, and facilitate algorithm sensitivity studies. The sizes of images and image analysis results in pathology image analysis pose significant challenges in algorithm evaluation. We present an efficient parallel spatial database approach to model, normalize, manage, and query large volumes of analytical image result data. This provides an efficient platform for algorithm evaluation. Our experiments with a set of brain tumor images demonstrate the application, scalability, and effectiveness of the platform. Context: The paper describes an approach and platform for evaluation of pathology image analysis algorithms. The platform facilitates algorithm evaluation through a high-performance database built on the Pathology Analytic Imaging Standards (PAIS) data model. Aims: (1) Develop a framework to support algorithm evaluation by modeling and managing analytical results and human annotations from pathology images; (2) Create a robust data normalization tool for converting, validating, and fixing spatial data from algorithm or human annotations; (3) Develop a set of queries to support data sampling and result comparisons; (4) Achieve high performance computation capacity via a parallel data management infrastructure, parallel data loading and spatial indexing optimizations in this infrastructure. Materials and Methods: We have considered two scenarios for algorithm evaluation: (1) algorithm comparison where multiple result sets from different methods are compared and consolidated; and (2) algorithm validation where algorithm results are compared with human annotations. We have developed a spatial normalization toolkit to validate and normalize spatial boundaries produced by image analysis algorithms or human annotations. The validated data were formatted based on the PAIS data model and loaded into a spatial database. To support efficient data loading, we have implemented a parallel data loading tool that takes advantage of multi-core CPUs to accelerate data injection. The spatial database manages both geometric shapes and image features or classifications, and enables spatial sampling, result comparison, and result aggregation through expressive structured query language (SQL) queries with spatial extensions. To provide scalable and efficient query support, we have employed a shared nothing parallel database architecture, which distributes data homogenously across multiple database partitions to take advantage of parallel computation power and implements spatial indexing to achieve high I/O throughput. Results: Our work proposes a high performance, parallel spatial database platform for algorithm validation and comparison. This platform was evaluated by storing, managing, and comparing analysis results from a set of brain tumor whole slide images. The tools we develop are open source and available to download. Conclusions: Pathology image algorithm validation and comparison are essential to iterative algorithm development and refinement. One critical component is the support for queries involving spatial predicates and comparisons. In our work, we develop an efficient data model and parallel database approach to model, normalize, manage and query large volumes of analytical image result data. Our experiments demonstrate that the data partitioning strategy and the grid-based indexing result in good data distribution across database nodes and reduce I/O overhead in spatial join queries through parallel retrieval of relevant data and quick subsetting of datasets. The set of tools in the framework provide a full pipeline to normalize, load, manage and query analytical results for algorithm evaluation. PMID:23599905

On compensation of mismatched recording conditions in the Bayesian approach for forensic automatic speaker recognition.

PubMed

Botti, F; Alexander, A; Drygajlo, A

2004-12-02

This paper deals with a procedure to compensate for mismatched recording conditions in forensic speaker recognition, using a statistical score normalization. Bayesian interpretation of the evidence in forensic automatic speaker recognition depends on three sets of recordings in order to perform forensic casework: reference (R) and control (C) recordings of the suspect, and a potential population database (P), as well as a questioned recording (QR) . The requirement of similar recording conditions between suspect control database (C) and the questioned recording (QR) is often not satisfied in real forensic cases. The aim of this paper is to investigate a procedure of normalization of scores, which is based on an adaptation of the Test-normalization (T-norm) [2] technique used in the speaker verification domain, to compensate for the mismatch. Polyphone IPSC-02 database and ASPIC (an automatic speaker recognition system developed by EPFL and IPS-UNIL in Lausanne, Switzerland) were used in order to test the normalization procedure. Experimental results for three different recording condition scenarios are presented using Tippett plots and the effect of the compensation on the evaluation of the strength of the evidence is discussed.

Using Virtual Servers to Teach the Implementation of Enterprise-Level DBMSs: A Teaching Note

ERIC Educational Resources Information Center

Wagner, William P.; Pant, Vik

2010-01-01

One of the areas where demand has remained strong for MIS students is in the area of database management. Since the early days, this topic has been a mainstay in the MIS curriculum. Students of database management today typically learn about relational databases, SQL, normalization, and how to design and implement various kinds of database…

The prediction of nonlinear dynamic loads on helicopters from flight variables using artificial neural networks

NASA Technical Reports Server (NTRS)

Cook, A. B.; Fuller, C. R.; O'Brien, W. F.; Cabell, R. H.

1992-01-01

A method of indirectly monitoring component loads through common flight variables is proposed which requires an accurate model of the underlying nonlinear relationships. An artificial neural network (ANN) model learns relationships through exposure to a database of flight variable records and corresponding load histories from an instrumented military helicopter undergoing standard maneuvers. The ANN model, utilizing eight standard flight variables as inputs, is trained to predict normalized time-varying mean and oscillatory loads on two critical components over a range of seven maneuvers. Both interpolative and extrapolative capabilities are demonstrated with agreement between predicted and measured loads on the order of 90 percent to 95 percent. This work justifies pursuing the ANN method of predicting loads from flight variables.

The Main Anatomic Variations of the Hepatic Artery and Their Importance in Surgical Practice: Review of the Literature.

PubMed

Noussios, George; Dimitriou, Ioannis; Chatzis, Iosif; Katsourakis, Anastasios

2017-04-01

Anatomical variations of the hepatic artery are important in the planning and performance of abdominal surgical procedures. Normal hepatic anatomy occurs in approximately 80% of cases, for the remaining 20% multiple variations have been described. The purpose of this study was to review the existing literature on the hepatic anatomy and to stress out its importance in surgical practice. Two main databases were searched for eligible articles during the period 2000 - 2015, and results concerning more than 19,000 patients were included in the study. The most common variation was the replaced right hepatic artery (type III according to Michels classification) which is the chief source of blood supply to the bile duct.

Handwritten word preprocessing for database adaptation

NASA Astrophysics Data System (ADS)

Oprean, Cristina; Likforman-Sulem, Laurence; Mokbel, Chafic

2013-01-01

Handwriting recognition systems are typically trained using publicly available databases, where data have been collected in controlled conditions (image resolution, paper background, noise level,...). Since this is not often the case in real-world scenarios, classification performance can be affected when novel data is presented to the word recognition system. To overcome this problem, we present in this paper a new approach called database adaptation. It consists of processing one set (training or test) in order to adapt it to the other set (test or training, respectively). Specifically, two kinds of preprocessing, namely stroke thickness normalization and pixel intensity normalization are considered. The advantage of such approach is that we can re-use the existing recognition system trained on controlled data. We conduct several experiments with the Rimes 2011 word database and with a real-world database. We adapt either the test set or the training set. Results show that training set adaptation achieves better results than test set adaptation, at the cost of a second training stage on the adapted data. Accuracy of data set adaptation is increased by 2% to 3% in absolute value over no adaptation.

Central Appalachian basin natural gas database: distribution, composition, and origin of natural gases

USGS Publications Warehouse

Román Colón, Yomayra A.; Ruppert, Leslie F.

2015-01-01

The U.S. Geological Survey (USGS) has compiled a database consisting of three worksheets of central Appalachian basin natural gas analyses and isotopic compositions from published and unpublished sources of 1,282 gas samples from Kentucky, Maryland, New York, Ohio, Pennsylvania, Tennessee, Virginia, and West Virginia. The database includes field and reservoir names, well and State identification number, selected geologic reservoir properties, and the composition of natural gases (methane; ethane; propane; butane, iso-butane [i-butane]; normal butane [n-butane]; iso-pentane [i-pentane]; normal pentane [n-pentane]; cyclohexane, and hexanes). In the first worksheet, location and American Petroleum Institute (API) numbers from public or published sources are provided for 1,231 of the 1,282 gas samples. A second worksheet of 186 gas samples was compiled from published sources and augmented with public location information and contains carbon, hydrogen, and nitrogen isotopic measurements of natural gas. The third worksheet is a key for all abbreviations in the database. The database can be used to better constrain the stratigraphic distribution, composition, and origin of natural gas in the central Appalachian basin.

Hypertension types defined by clinic and ambulatory blood pressure in 14 143 patients referred to hypertension clinics worldwide. Data from the ARTEMIS study.

PubMed

Omboni, Stefano; Aristizabal, Dagnovar; De la Sierra, Alejandro; Dolan, Eamon; Head, Geoffrey; Kahan, Thomas; Kantola, Ilkka; Kario, Kazuomi; Kawecka-Jaszcz, Kalina; Malan, Leoné; Narkiewicz, Krzysztof; Octavio, José A; Ohkubo, Takayoshi; Palatini, Paolo; Siègelovà, Jarmila; Silva, Eglé; Stergiou, George; Zhang, Yuqing; Mancia, Giuseppe; Parati, Gianfranco

2016-11-01

The Ambulatory blood pressure Registry TEleMonitoring of hypertension and cardiovascular rISk project was designed to set up an international registry including clinic blood pressure (CBP) and ambulatory blood pressure (ABP) measurements in patients attending hypertension clinics in all five continents, aiming to assess different daily life hypertension types. Cross-sectional ABP, CBP and demographic data, medical history and cardiovascular risk profile were provided from existing databases by hypertension clinics. Hypertension types were evaluated considering CBP (≥140/90 mmHg) and 24-h ABP (≥130/80 mmHg). Overall, 14 143 patients from 27 countries across all five continents were analyzed (Europe 73%, Africa 3%, America 9%, Asia 14% and Australia 2%). Mean age was 57 ± 14 years, men 51%, treated for hypertension 46%, cardiovascular disease 14%, people with diabetes 14%, dyslipidemia 33% and smokers 19%. The prevalence of hypertension was higher by CBP than by ABP monitoring (72 vs. 60%, P < 0.0001). Sustained hypertension (elevated CBP and ABP) was detected in 49% of patients. White-coat hypertension (WCH, elevated CBP with normal ABP) was more common than masked hypertension (elevated ABP with normal CBP) (23 vs. 10%; P < 0.0001). Sustained hypertension was more common in Europe and America and in elderly, men, obese patients with cardiovascular comorbidities. WCH was less common in Australia, America and Africa, and more common in elderly, obese women. Masked hypertension was more common in Asia and in men with diabetes. Smoking was a determinant for sustained hypertension and masked hypertension. Our analysis showed an unbalanced distribution of WCH and masked hypertension patterns among different continents, suggesting an interplay of genetic and environmental factors, and likely also different healthcare administrative and practice patterns.

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2012 CFR

2012-04-01

... places that information into a common database that the covered affiliate may access. (3) Service... maintains or accesses a common database that the covered affiliate may access) receives eligibility... the notice and opt-out provisions under other privacy rules under the FCRA, the GLB Act or the CEA. ...

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2013 CFR

2013-04-01

... places that information into a common database that the covered affiliate may access. (3) Service... maintains or accesses a common database that the covered affiliate may access) receives eligibility... the notice and opt-out provisions under other privacy rules under the FCRA, the GLB Act or the CEA. ...

17 CFR 162.3 - Affiliate marketing opt out and exceptions.

Code of Federal Regulations, 2014 CFR

2014-04-01

... places that information into a common database that the covered affiliate may access. (3) Service... maintains or accesses a common database that the covered affiliate may access) receives eligibility... the notice and opt-out provisions under other privacy rules under the FCRA, the GLB Act or the CEA. ...

DEVELOPMENT OF THE METHOD AND U.S. NORMALIZATION DATABASE FOR LIFE CYCLE IMPACT ASSESSMENT AND SUSTAINABILITY METRICS

EPA Science Inventory

Normalization is an optional step within Life Cycle Impact Assessment (LCIA) that may be used to assist in the interpretation of life cycle inventory data as well as, life cycle impact assessment results. Normalization transforms the magnitude of LCI and LCIA results into relati...

Evaluation of a speaker identification system with and without fusion using three databases in the presence of noise and handset effects

NASA Astrophysics Data System (ADS)

S. Al-Kaltakchi, Musab T.; Woo, Wai L.; Dlay, Satnam; Chambers, Jonathon A.

2017-12-01

In this study, a speaker identification system is considered consisting of a feature extraction stage which utilizes both power normalized cepstral coefficients (PNCCs) and Mel frequency cepstral coefficients (MFCC). Normalization is applied by employing cepstral mean and variance normalization (CMVN) and feature warping (FW), together with acoustic modeling using a Gaussian mixture model-universal background model (GMM-UBM). The main contributions are comprehensive evaluations of the effect of both additive white Gaussian noise (AWGN) and non-stationary noise (NSN) (with and without a G.712 type handset) upon identification performance. In particular, three NSN types with varying signal to noise ratios (SNRs) were tested corresponding to street traffic, a bus interior, and a crowded talking environment. The performance evaluation also considered the effect of late fusion techniques based on score fusion, namely, mean, maximum, and linear weighted sum fusion. The databases employed were TIMIT, SITW, and NIST 2008; and 120 speakers were selected from each database to yield 3600 speech utterances. As recommendations from the study, mean fusion is found to yield overall best performance in terms of speaker identification accuracy (SIA) with noisy speech, whereas linear weighted sum fusion is overall best for original database recordings.

Chinese herbal medicines for benign thyroid nodules in adults.

PubMed

Wu, Wenxun; Yin, Detao; Yang, Weimin; Kan, Quancheng; Liu, Zhangsuo; Ren, Xiaoyan; Zhai, Chenguang; Zhang, Shengjun

2014-03-04

A thyroid nodule is a discrete lesion within the thyroid gland that might be palpable and is ultrasonographically distinct from the surrounding thyroid parenchyma. Thyroid nodules are more common as age increases and occur more frequently in women. Benign thyroid nodules often cause pressure symptoms and cosmetic complaints. In China and many other countries, doctors use Chinese herbal medicines (CHM) to treat thyroid nodules. To assess the effects of Chinese herbal medicines in the treatment of benign thyroid nodules in adults. Review authors searched the following electronic databases: The Cochrane Library, MEDLINE, EMBASE, the Chinese Biomedical Literature Database (CBM), the China National Knowledge Infrastructure (CNKI), VIP information (a Chinese database), WANFANG Data (a Chinese database), the Chinese Conference Papers Database and the Chinese Dissertation Database (all searched up to April 2013). Randomised controlled trials comparing CHM or CHM plus levothyroxine versus levothyroxine, placebo or no treatment in adults with benign thyroid nodules. Two review authors independently extracted data, assessed studies for risk of bias and evaluated overall study quality according to GRADE (Grading of Recommendations Assessment, Development and Evaluation), with differences resolved by consensus. We included one randomised trial involving 152 participants with a randomisation ratio of 2:1 (CHM vs no treatment). The trial applied adequate sequence generation; however, allocation concealment was unclear. Duration of treatment was three months, and follow-up six months. Our a priori defined outcomes of interest (i.e. nodule volume reduction ≥ 50%; pressure symptoms, cosmetic complaints or both; health-related quality of life; all-cause mortality; cancer occurrence; changes in number and size of thyroid nodules; changes in thyroid volume; and socioeconomic effects) were not investigated in the included study. Thyrotropin (TSH), thyroxine (T4) and tri-iodothyronine (T3) serum levels were normal in both groups before and after the trial was conducted. No adverse events were reported (low quality evidence). Firm evidence cannot be found to support or refute the use of Chinese herbal medicines for benign thyroid nodules in adults.

Challenges in developing medicinal plant databases for sharing ethnopharmacological knowledge.

PubMed

Ningthoujam, Sanjoy Singh; Talukdar, Anupam Das; Potsangbam, Kumar Singh; Choudhury, Manabendra Dutta

2012-05-07

Major research contributions in ethnopharmacology have generated vast amount of data associated with medicinal plants. Computerized databases facilitate data management and analysis making coherent information available to researchers, planners and other users. Web-based databases also facilitate knowledge transmission and feed the circle of information exchange between the ethnopharmacological studies and public audience. However, despite the development of many medicinal plant databases, a lack of uniformity is still discernible. Therefore, it calls for defining a common standard to achieve the common objectives of ethnopharmacology. The aim of the study is to review the diversity of approaches in storing ethnopharmacological information in databases and to provide some minimal standards for these databases. Survey for articles on medicinal plant databases was done on the Internet by using selective keywords. Grey literatures and printed materials were also searched for information. Listed resources were critically analyzed for their approaches in content type, focus area and software technology. Necessity for rapid incorporation of traditional knowledge by compiling primary data has been felt. While citation collection is common approach for information compilation, it could not fully assimilate local literatures which reflect traditional knowledge. Need for defining standards for systematic evaluation, checking quality and authenticity of the data is felt. Databases focussing on thematic areas, viz., traditional medicine system, regional aspect, disease and phytochemical information are analyzed. Issues pertaining to data standard, data linking and unique identification need to be addressed in addition to general issues like lack of update and sustainability. In the background of the present study, suggestions have been made on some minimum standards for development of medicinal plant database. In spite of variations in approaches, existence of many overlapping features indicates redundancy of resources and efforts. As the development of global data in a single database may not be possible in view of the culture-specific differences, efforts can be given to specific regional areas. Existing scenario calls for collaborative approach for defining a common standard in medicinal plant database for knowledge sharing and scientific advancement. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

Second Line of Defense Master Spares Catalog

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

Henderson, Dale L.; Muller, George; Mercier, Theresa M.

This catalog is intended to be a comprehensive listing of repair parts, components, kits, and consumable items used on the equipment deployed at SLD sites worldwide. The catalog covers detection, CAS, network, ancillary equipment, and tools. The catalog is backed by a Master Parts Database which is used to generate the standard report views of the catalog. The master parts database is a relational database containing a record for every part in the master parts catalog along with supporting tables for normalizing fields in the records. The database also includes supporting queries, database maintenance forms, and reports.

An integrated command control and communications center for first responders

NASA Astrophysics Data System (ADS)

Messner, Richard A.; Hludik, Frank; Vidacic, Dragan; Melnyk, Pavlo

2005-05-01

First responders to a major incident include many different agencies. These may include law enforcement officers, multiple fire departments, paramedics, HAZMAT response teams, and possibly even federal personnel such as FBI and FEMA. Often times multiple jurisdictions respond to the incident which causes interoperability issues with respect to communication and dissemination of time critical information. Accurate information from all responding sources needs to be rapidly collected and made available to the current on site responders as well as the follow-on responders who may just be arriving on scene. The creation of a common central database with a simple easy to use interface that is dynamically updated in real time would allow prompt and efficient information distribution between different jurisdictions. Such a system is paramount to the success of any response to a major incident. First responders typically arrive in mobile vehicles that are equipped with communications equipment. Although the first responders may make reports back to their specific home based command centers, the details of those reports are not typically available to other first responders who are not a part of that agencies infrastructure. Furthermore, the collection of information often occurs outside of the first responder vehicle and the details of the scene are normally either radioed from the field or written down and then disseminated after significant delay. Since first responders are not usually on the same communications channels, and the fact that there is normally a considerable amount of confusion during the first few hours on scene, it would be beneficial if there were a centralized location for the repository of time critical information which could be accessed by all the first responders in a common fashion without having to redesign or add significantly to each first responders hardware/software systems. Each first responder would then be able to provide information regarding their particular situation and such information could be accessed by all responding personnel. This will require the transmission of information provided by the first responder to a common central database system. In order to fully investigate the use of technology, it is advantageous to build a test bed in order to evaluate the proper hardware/software necessary, and explore the envisioned scenarios of operation before deployment of an actual system. This paper describes an ongoing effort at the University of New Hampshire to address these emergency responder needs.

Genome-wide association as a means to understanding the mammary gland

USDA-ARS?s Scientific Manuscript database

Next-generation sequencing and related technologies have facilitated the creation of enormous public databases that catalogue genomic variation. These databases have facilitated a variety of approaches to discover new genes that regulate normal biology as well as disease. Genome wide association (...

Acoustic analysis of normal Saudi adult voices.

PubMed

Malki, Khalid H; Al-Habib, Salman F; Hagr, Abulrahman A; Farahat, Mohamed M

2009-08-01

To determine the acoustic differences between Saudi adult male and female voices, and to compare the acoustic variables of the Multidimensional Voice Program (MDVP) obtained from North American adults to a group of Saudi males and females. A cross-sectional survey of normal adult male and female voices was conducted at King Abdulaziz University Hospital, Riyadh, Kingdom of Saudi Arabia between March 2007 and December 2008. Ninety-five Saudi subjects sustained the vowel /a/ 6 times, and the steady state portion of 3 samples was analyzed and compared with the samples of the KayPentax normative voice database. Significant differences were found between Saudi and North American KayPentax database groups. In the male subjects, 15 of 33 MDVP variables, and 10 of 33 variables in the female subjects were found to be significantly different from the KayPentax database. We conclude that the acoustical differences may reflect laryngeal anatomical or tissue differences between the Saudi and the KayPentax database.

Risk Factors for Post-treatment Complex Regional Pain Syndrome (CRPS): An Analysis of 647 Cases of CRPS from the Danish Patient Compensation Association.

PubMed

Petersen, Pelle B; Mikkelsen, Kim L; Lauritzen, Jes B; Krogsgaard, Michael R

2018-03-01

Complex regional pain syndrome is a challenging condition that includes a broad spectrum of sensory, autonomic, and motor features predominantly in extremities recovering from a trauma. Few large-scale studies have addressed occurrence of and factors associated with complex regional pain syndrome (CRPS) following orthopedic treatment. The present study aimed to identify factors associated with post-treatment development of CRPS. Using the Danish Patient Compensation Association's database, we identified 647 patients claiming post-treatment CRPS between 1992 and 2015. Age, gender, initial diagnosis, treatment, and amount of compensation were extracted. Multivariate logistic regressions were performed to identify variables associated with approval of the claim. For carpal tunnel syndrome (CTS) patients, we registered whether symptoms were bilateral or unilateral and if neurophysiology prior to treatment was pathologic. The following ratios were found: women:men was 4:1, primary diagnosis to the upper limb:lower limb was 2.5:1, and surgical:nonsurgical treatment was 3:1. Mean age was 47.5 ± 13.7 years, and no intergender difference was detected. Antebrachial fracture (23%) and CTS (9%) were the most common primary conditions. Surgical treatment was associated with approval of the claim (odds ratio 3.5, 95% confidence interval 2.3 to 5.3; P < 0.001). Half of CTS patients had normal neurophysiology prior to surgery; among patients with unilateral symptoms, 71.4% had normal neurophysiology. Female gender, surgical treatment, and treatment to the upper limb were risk factors. Elective surgery accounted for a large number of post-treatment CRPS patients. In CTS patients developing CRPS, normal neurophysiological examination findings were common, and it could be suspected that these patients were suffering from an pre-clinical stage of CRPS, not CTS. © 2017 World Institute of Pain.

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis

PubMed Central

Bagger, Frederik Otzen; Sasivarevic, Damir; Sohi, Sina Hadi; Laursen, Linea Gøricke; Pundhir, Sachin; Sønderby, Casper Kaae; Winther, Ole; Rapin, Nicolas; Porse, Bo T.

2016-01-01

Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan–Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space. PMID:26507857

Information Literacy Skills: Comparing and Evaluating Databases

ERIC Educational Resources Information Center

Grismore, Brian A.

2012-01-01

The purpose of this database comparison is to express the importance of teaching information literacy skills and to apply those skills to commonly used Internet-based research tools. This paper includes a comparison and evaluation of three databases (ProQuest, ERIC, and Google Scholar). It includes strengths and weaknesses of each database based…

Teaching Advanced SQL Skills: Text Bulk Loading

ERIC Educational Resources Information Center

Olsen, David; Hauser, Karina

2007-01-01

Studies show that advanced database skills are important for students to be prepared for today's highly competitive job market. A common task for database administrators is to insert a large amount of data into a database. This paper illustrates how an up-to-date, advanced database topic, namely bulk insert, can be incorporated into a database…

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.

Detection of Pathological Voice Using Cepstrum Vectors: A Deep Learning Approach.

PubMed

Fang, Shih-Hau; Tsao, Yu; Hsiao, Min-Jing; Chen, Ji-Ying; Lai, Ying-Hui; Lin, Feng-Chuan; Wang, Chi-Te

2018-03-19

Computerized detection of voice disorders has attracted considerable academic and clinical interest in the hope of providing an effective screening method for voice diseases before endoscopic confirmation. This study proposes a deep-learning-based approach to detect pathological voice and examines its performance and utility compared with other automatic classification algorithms. This study retrospectively collected 60 normal voice samples and 402 pathological voice samples of 8 common clinical voice disorders in a voice clinic of a tertiary teaching hospital. We extracted Mel frequency cepstral coefficients from 3-second samples of a sustained vowel. The performances of three machine learning algorithms, namely, deep neural network (DNN), support vector machine, and Gaussian mixture model, were evaluated based on a fivefold cross-validation. Collective cases from the voice disorder database of MEEI (Massachusetts Eye and Ear Infirmary) were used to verify the performance of the classification mechanisms. The experimental results demonstrated that DNN outperforms Gaussian mixture model and support vector machine. Its accuracy in detecting voice pathologies reached 94.26% and 90.52% in male and female subjects, based on three representative Mel frequency cepstral coefficient features. When applied to the MEEI database for validation, the DNN also achieved a higher accuracy (99.32%) than the other two classification algorithms. By stacking several layers of neurons with optimized weights, the proposed DNN algorithm can fully utilize the acoustic features and efficiently differentiate between normal and pathological voice samples. Based on this pilot study, future research may proceed to explore more application of DNN from laboratory and clinical perspectives. Copyright © 2018 The Voice Foundation. Published by Elsevier Inc. All rights reserved.

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

Habte, A.; Lopez, A.; Sengupta, M.

Typical Meteorological Year (TMY) data sets provide industry standard resource information for building designers and are commonly used by the solar industry to estimate photovoltaic and concentrating solar power system performance. Historically, TMY data sets were only available for certain station locations, but current TMY data sets are available on the same grid as the National Solar Radiation Database data and are referred to as the gridded TMY. In this report, a comparison of TMY, typical direct (normal irradiance) year (TDY), and typical global (horizontal irradiance) year (TGY) data sets were performed to better understand the impact of ancillary weathermore » variables upon them. These analyses identified geographical areas of high and low temporal and spatial variability, thereby providing insight into the representativeness of a particular TMY data set for use in renewable energy as well as other applications.« less

The Main Anatomical Variations of the Pancreatic Duct System: Review of the Literature and Its Importance in Surgical Practice.

PubMed

Dimitriou, Ioannis; Katsourakis, Anastasios; Nikolaidou, Eirini; Noussios, George

2018-05-01

Anatomical variations or anomalies of the pancreatic ducts are important in the planning and performance of endoscopic retrograde cholangiopancreatography (ERCP) and surgical procedures of the pancreas. Normal pancreatic duct anatomy occurs in approximately 94.3% of cases, and multiple variations have been described for the remaining 5.7%. The purpose of this study was to review the literature on the pancreatic duct anatomy and to underline its importance in daily invasive endoscopic and surgical practice. Two main databases were searched for suitable articles published from 2000 to 2017, and results concerning more than 8,200 patients were included in the review. The most common anatomical variation was that of pancreas divisum, which appeared in approximately 4.5% of cases.

The Common Gateway Interface (CGI) for Enhancing Access to Database Servers via the World Wide Web (WWW).

ERIC Educational Resources Information Center

Machovec, George S., Ed.

1995-01-01

Explains the Common Gateway Interface (CGI) protocol as a set of rules for passing information from a Web server to an external program such as a database search engine. Topics include advantages over traditional client/server solutions, limitations, sample library applications, and sources of information from the Internet. (LRW)

Development of Vision Based Multiview Gait Recognition System with MMUGait Database

PubMed Central

Ng, Hu; Tan, Wooi-Haw; Tong, Hau-Lee

2014-01-01

This paper describes the acquisition setup and development of a new gait database, MMUGait. This database consists of 82 subjects walking under normal condition and 19 subjects walking with 11 covariate factors, which were captured under two views. This paper also proposes a multiview model-based gait recognition system with joint detection approach that performs well under different walking trajectories and covariate factors, which include self-occluded or external occluded silhouettes. In the proposed system, the process begins by enhancing the human silhouette to remove the artifacts. Next, the width and height of the body are obtained. Subsequently, the joint angular trajectories are determined once the body joints are automatically detected. Lastly, crotch height and step-size of the walking subject are determined. The extracted features are smoothened by Gaussian filter to eliminate the effect of outliers. The extracted features are normalized with linear scaling, which is followed by feature selection prior to the classification process. The classification experiments carried out on MMUGait database were benchmarked against the SOTON Small DB from University of Southampton. Results showed correct classification rate above 90% for all the databases. The proposed approach is found to outperform other approaches on SOTON Small DB in most cases. PMID:25143972

The research infrastructure of Chinese foundations, a database for Chinese civil society studies

PubMed Central

Ma, Ji; Wang, Qun; Dong, Chao; Li, Huafang

2017-01-01

This paper provides technical details and user guidance on the Research Infrastructure of Chinese Foundations (RICF), a database of Chinese foundations, civil society, and social development in general. The structure of the RICF is deliberately designed and normalized according to the Three Normal Forms. The database schema consists of three major themes: foundations’ basic organizational profile (i.e., basic profile, board member, supervisor, staff, and related party tables), program information (i.e., program information, major program, program relationship, and major recipient tables), and financial information (i.e., financial position, financial activities, cash flow, activity overview, and large donation tables). The RICF’s data quality can be measured by four criteria: data source reputation and credibility, completeness, accuracy, and timeliness. Data records are properly versioned, allowing verification and replication for research purposes. PMID:28742065

Indian genetic disease database

PubMed Central

Pradhan, Sanchari; Sengupta, Mainak; Dutta, Anirban; Bhattacharyya, Kausik; Bag, Sumit K.; Dutta, Chitra; Ray, Kunal

2011-01-01

Indians, representing about one-sixth of the world population, consist of several thousands of endogamous groups with strong potential for excess of recessive diseases. However, no database is available on Indian population with comprehensive information on the diseases common in the country. To address this issue, we present Indian Genetic Disease Database (IGDD) release 1.0 (http://www.igdd.iicb.res.in)—an integrated and curated repository of growing number of mutation data on common genetic diseases afflicting the Indian populations. Currently the database covers 52 diseases with information on 5760 individuals carrying the mutant alleles of causal genes. Information on locus heterogeneity, type of mutation, clinical and biochemical data, geographical location and common mutations are furnished based on published literature. The database is currently designed to work best with Internet Explorer 8 (optimal resolution 1440 × 900) and it can be searched based on disease of interest, causal gene, type of mutation and geographical location of the patients or carriers. Provisions have been made for deposition of new data and logistics for regular updation of the database. The IGDD web portal, planned to be made freely available, contains user-friendly interfaces and is expected to be highly useful to the geneticists, clinicians, biologists and patient support groups of various genetic diseases. PMID:21037256

ADVICE--Educational System for Teaching Database Courses

ERIC Educational Resources Information Center

Cvetanovic, M.; Radivojevic, Z.; Blagojevic, V.; Bojovic, M.

2011-01-01

This paper presents a Web-based educational system, ADVICE, that helps students to bridge the gap between database management system (DBMS) theory and practice. The usage of ADVICE is presented through a set of laboratory exercises developed to teach students conceptual and logical modeling, SQL, formal query languages, and normalization. While…

SSME environment database development

NASA Technical Reports Server (NTRS)

Reardon, John

1987-01-01

The internal environment of the Space Shuttle Main Engine (SSME) is being determined from hot firings of the prototype engines and from model tests using either air or water as the test fluid. The objectives are to develop a database system to facilitate management and analysis of test measurements and results, to enter available data into the the database, and to analyze available data to establish conventions and procedures to provide consistency in data normalization and configuration geometry references.

Distribution Characteristics of Air-Bone Gaps – Evidence of Bias in Manual Audiometry

PubMed Central

Margolis, Robert H.; Wilson, Richard H.; Popelka, Gerald R.; Eikelboom, Robert H.; Swanepoel, De Wet; Saly, George L.

2015-01-01

Objective Five databases were mined to examine distributions of air-bone gaps obtained by automated and manual audiometry. Differences in distribution characteristics were examined for evidence of influences unrelated to the audibility of test signals. Design The databases provided air- and bone-conduction thresholds that permitted examination of air-bone gap distributions that were free of ceiling and floor effects. Cases with conductive hearing loss were eliminated based on air-bone gaps, tympanometry, and otoscopy, when available. The analysis is based on 2,378,921 threshold determinations from 721,831 subjects from five databases. Results Automated audiometry produced air-bone gaps that were normally distributed suggesting that air- and bone-conduction thresholds are normally distributed. Manual audiometry produced air-bone gaps that were not normally distributed and show evidence of biasing effects of assumptions of expected results. In one database, the form of the distributions showed evidence of inclusion of conductive hearing losses. Conclusions Thresholds obtained by manual audiometry show tester bias effects from assumptions of the patient’s hearing loss characteristics. Tester bias artificially reduces the variance of bone-conduction thresholds and the resulting air-bone gaps. Because the automated method is free of bias from assumptions of expected results, these distributions are hypothesized to reflect the true variability of air- and bone-conduction thresholds and the resulting air-bone gaps. PMID:26627469

GlycoRDF: an ontology to standardize glycomics data in RDF

PubMed Central

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F.; Campbell, Matthew P.; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-01-01

Motivation: Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. Results: An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. Availability and implementation: The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). Contact: rene@ccrc.uga.edu or kkiyoko@soka.ac.jp Supplementary information: Supplementary data are available at Bioinformatics online. PMID:25388145

GlycoRDF: an ontology to standardize glycomics data in RDF.

PubMed

Ranzinger, Rene; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P; Kawano, Shin; Lütteke, Thomas; Okuda, Shujiro; Shinmachi, Daisuke; Shikanai, Toshihide; Sawaki, Hiromichi; Toukach, Philip; Matsubara, Masaaki; Yamada, Issaku; Narimatsu, Hisashi

2015-03-15

Over the last decades several glycomics-based bioinformatics resources and databases have been created and released to the public. Unfortunately, there is no common standard in the representation of the stored information or a common machine-readable interface allowing bioinformatics groups to easily extract and cross-reference the stored information. An international group of bioinformatics experts in the field of glycomics have worked together to create a standard Resource Description Framework (RDF) representation for glycomics data, focused on glycan sequences and related biological source, publications and experimental data. This RDF standard is defined by the GlycoRDF ontology and will be used by database providers to generate common machine-readable exports of the data stored in their databases. The ontology, supporting documentation and source code used by database providers to generate standardized RDF are available online (http://www.glycoinfo.org/GlycoRDF/). © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Common Core of Data (CCD): School Years 1996-1997 through 2000-2001. [CD-ROM].

ERIC Educational Resources Information Center

National Center for Education Statistics (ED), Washington, DC.

The Common Core of Data (CCD) is NCES's primary database on elementary and secondary public education in the United States. CCD is a comprehensive, annual, national statistical database of all elementary and secondary schools and school districts, which contains data that are comparable across all states. The 50 states and the District of Columbia…

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases with a common or coordinated reference system, that can be used to geolocate all database information...

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2010 CFR

2010-04-01

... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases with a common or coordinated reference system, that can be used to geolocate all database information...

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases with a common or coordinated reference system, that can be used to geolocate all database information...

23 CFR 971.204 - Management systems requirements.

Code of Federal Regulations, 2013 CFR

2013-04-01

... maintain the management systems and their associated databases; and (5) A process for data collection, processing, analysis, and updating for each management system. (c) All management systems will use databases with a common or coordinated reference system, that can be used to geolocate all database information...

TRY – a global database of plant traits

PubMed Central

Kattge, J; Díaz, S; Lavorel, S; Prentice, I C; Leadley, P; Bönisch, G; Garnier, E; Westoby, M; Reich, P B; Wright, I J; Cornelissen, J H C; Violle, C; Harrison, S P; Van Bodegom, P M; Reichstein, M; Enquist, B J; Soudzilovskaia, N A; Ackerly, D D; Anand, M; Atkin, O; Bahn, M; Baker, T R; Baldocchi, D; Bekker, R; Blanco, C C; Blonder, B; Bond, W J; Bradstock, R; Bunker, D E; Casanoves, F; Cavender-Bares, J; Chambers, J Q; Chapin, F S; Chave, J; Coomes, D; Cornwell, W K; Craine, J M; Dobrin, B H; Duarte, L; Durka, W; Elser, J; Esser, G; Estiarte, M; Fagan, W F; Fang, J; Fernández-Méndez, F; Fidelis, A; Finegan, B; Flores, O; Ford, H; Frank, D; Freschet, G T; Fyllas, N M; Gallagher, R V; Green, W A; Gutierrez, A G; Hickler, T; Higgins, S I; Hodgson, J G; Jalili, A; Jansen, S; Joly, C A; Kerkhoff, A J; Kirkup, D; Kitajima, K; Kleyer, M; Klotz, S; Knops, J M H; Kramer, K; Kühn, I; Kurokawa, H; Laughlin, D; Lee, T D; Leishman, M; Lens, F; Lenz, T; Lewis, S L; Lloyd, J; Llusià, J; Louault, F; Ma, S; Mahecha, M D; Manning, P; Massad, T; Medlyn, B E; Messier, J; Moles, A T; Müller, S C; Nadrowski, K; Naeem, S; Niinemets, Ü; Nöllert, S; Nüske, A; Ogaya, R; Oleksyn, J; Onipchenko, V G; Onoda, Y; Ordoñez, J; Overbeck, G; Ozinga, W A; Patiño, S; Paula, S; Pausas, J G; Peñuelas, J; Phillips, O L; Pillar, V; Poorter, H; Poorter, L; Poschlod, P; Prinzing, A; Proulx, R; Rammig, A; Reinsch, S; Reu, B; Sack, L; Salgado-Negret, B; Sardans, J; Shiodera, S; Shipley, B; Siefert, A; Sosinski, E; Soussana, J-F; Swaine, E; Swenson, N; Thompson, K; Thornton, P; Waldram, M; Weiher, E; White, M; White, S; Wright, S J; Yguel, B; Zaehle, S; Zanne, A E; Wirth, C

2011-01-01

Plant traits – the morphological, anatomical, physiological, biochemical and phenological characteristics of plants and their organs – determine how primary producers respond to environmental factors, affect other trophic levels, influence ecosystem processes and services and provide a link from species richness to ecosystem functional diversity. Trait data thus represent the raw material for a wide range of research from evolutionary biology, community and functional ecology to biogeography. Here we present the global database initiative named TRY, which has united a wide range of the plant trait research community worldwide and gained an unprecedented buy-in of trait data: so far 93 trait databases have been contributed. The data repository currently contains almost three million trait entries for 69 000 out of the world's 300 000 plant species, with a focus on 52 groups of traits characterizing the vegetative and regeneration stages of the plant life cycle, including growth, dispersal, establishment and persistence. A first data analysis shows that most plant traits are approximately log-normally distributed, with widely differing ranges of variation across traits. Most trait variation is between species (interspecific), but significant intraspecific variation is also documented, up to 40% of the overall variation. Plant functional types (PFTs), as commonly used in vegetation models, capture a substantial fraction of the observed variation – but for several traits most variation occurs within PFTs, up to 75% of the overall variation. In the context of vegetation models these traits would better be represented by state variables rather than fixed parameter values. The improved availability of plant trait data in the unified global database is expected to support a paradigm shift from species to trait-based ecology, offer new opportunities for synthetic plant trait research and enable a more realistic and empirically grounded representation of terrestrial vegetation in Earth system models.

The LISS--a public database of common imaging signs of lung diseases for computer-aided detection and diagnosis research and medical education.

PubMed

Han, Guanghui; Liu, Xiabi; Han, Feifei; Santika, I Nyoman Tenaya; Zhao, Yanfeng; Zhao, Xinming; Zhou, Chunwu

2015-02-01

Lung computed tomography (CT) imaging signs play important roles in the diagnosis of lung diseases. In this paper, we review the significance of CT imaging signs in disease diagnosis and determine the inclusion criterion of CT scans and CT imaging signs of our database. We develop the software of abnormal regions annotation and design the storage scheme of CT images and annotation data. Then, we present a publicly available database of lung CT imaging signs, called LISS for short, which contains 271 CT scans and 677 abnormal regions in them. The 677 abnormal regions are divided into nine categories of common CT imaging signs of lung disease (CISLs). The ground truth of these CISLs regions and the corresponding categories are provided. Furthermore, to make the database publicly available, all private data in CT scans are eliminated or replaced with provisioned values. The main characteristic of our LISS database is that it is developed from a new perspective of CT imaging signs of lung diseases instead of commonly considered lung nodules. Thus, it is promising to apply to computer-aided detection and diagnosis research and medical education.

System for Performing Single Query Searches of Heterogeneous and Dispersed Databases

NASA Technical Reports Server (NTRS)

Maluf, David A. (Inventor); Okimura, Takeshi (Inventor); Gurram, Mohana M. (Inventor); Tran, Vu Hoang (Inventor); Knight, Christopher D. (Inventor); Trinh, Anh Ngoc (Inventor)

2017-01-01

The present invention is a distributed computer system of heterogeneous databases joined in an information grid and configured with an Application Programming Interface hardware which includes a search engine component for performing user-structured queries on multiple heterogeneous databases in real time. This invention reduces overhead associated with the impedance mismatch that commonly occurs in heterogeneous database queries.

BloodSpot: a database of gene expression profiles and transcriptional programs for healthy and malignant haematopoiesis.

PubMed

Bagger, Frederik Otzen; Sasivarevic, Damir; Sohi, Sina Hadi; Laursen, Linea Gøricke; Pundhir, Sachin; Sønderby, Casper Kaae; Winther, Ole; Rapin, Nicolas; Porse, Bo T

2016-01-04

Research on human and murine haematopoiesis has resulted in a vast number of gene-expression data sets that can potentially answer questions regarding normal and aberrant blood formation. To researchers and clinicians with limited bioinformatics experience, these data have remained available, yet largely inaccessible. Current databases provide information about gene-expression but fail to answer key questions regarding co-regulation, genetic programs or effect on patient survival. To address these shortcomings, we present BloodSpot (www.bloodspot.eu), which includes and greatly extends our previously released database HemaExplorer, a database of gene expression profiles from FACS sorted healthy and malignant haematopoietic cells. A revised interactive interface simultaneously provides a plot of gene expression along with a Kaplan-Meier analysis and a hierarchical tree depicting the relationship between different cell types in the database. The database now includes 23 high-quality curated data sets relevant to normal and malignant blood formation and, in addition, we have assembled and built a unique integrated data set, BloodPool. Bloodpool contains more than 2000 samples assembled from six independent studies on acute myeloid leukemia. Furthermore, we have devised a robust sample integration procedure that allows for sensitive comparison of user-supplied patient samples in a well-defined haematopoietic cellular space. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Musical hallucinations: a brief review of functional neuroimaging findings.

PubMed

Bernardini, Francesco; Attademo, Luigi; Blackmon, Karen; Devinsky, Orrin

2017-10-01

Musical hallucinations are uncommon phenomena characterized by intrusive and frequently distressful auditory musical percepts without an external source, often associated with hypoacusis, psychiatric illness, focal brain lesion, epilepsy, and intoxication/pharmacology. Their physiological basis is thought to involve diverse mechanisms, including "release" from normal sensory or inhibitory inputs as well as stimulation during seizures, or they can be produced by functional or structural disorders in diverse cortical and subcortical areas. The aim of this review is to further explore their pathophysiology, describing the functional neuroimaging findings regarding musical hallucinations. A literature search of the PubMed electronic database was conducted through to 29 December 2015. Search terms included "musical hallucinations" combined with the names of specific functional neuroimaging techniques. A total of 18 articles, all clinical case reports, providing data on 23 patients, comprised the set we reviewed. Diverse pathological processes and patient populations with musical hallucinations were included in the studies. Converging data from multiple studies suggest that the superior temporal sulcus is the most common site and that activation is the most common mechanism. Further neurobiological research is needed to clarify the pathophysiology of musical hallucinations.

An Adaptive Database Intrusion Detection System

ERIC Educational Resources Information Center

Barrios, Rita M.

2011-01-01

Intrusion detection is difficult to accomplish when attempting to employ current methodologies when considering the database and the authorized entity. It is a common understanding that current methodologies focus on the network architecture rather than the database, which is not an adequate solution when considering the insider threat. Recent…

Analysis of the Astronomy Diagnostic Test

ERIC Educational Resources Information Center

Brogt, Erik; Sabers, Darrell; Prather, Edward E.; Deming, Grace L.; Hufnagel, Beth; Slater, Timothy F.

2007-01-01

Seventy undergraduate class sections were examined from the database of Astronomy Diagnostic Test (ADT) results of Deming and Hufnagel to determine if course format correlated with ADT normalized gain scores. Normalized gains were calculated for four different classroom scenarios: lecture, lecture with discussion, lecture with lab, and lecture…

Population genetics of chronic kidney disease: the evolving story of APOL1.

PubMed

Wasser, Walter G; Tzur, Shay; Wolday, Dawit; Adu, Dwomoa; Baumstein, Donald; Rosset, Saharon; Skorecki, Karl

2012-01-01

Advances in human genome sequencing and generation of public databases of genomic diversity enable nephrologists to re-examine the genetics of common, complex kidney diseases. Non-diabetic kidney diseases prevalent in African ancestry populations and the allelic variation described in chromosome 22q12.3 is one such illustrative example. Newly available genomic database information enabled research groups to discover common functional DNA sequence risk variants in the APOL1 gene. These variants (termed G1 and G2) evolved to confer protection from a species of trypanosomal infection and thus achieved high prominence in many geographic regions of Africa and have been carried over to African diaspora communities worldwide. Since these discoveries two years ago, new insights have been gained: localization of APOL1 in normal and disease kidney tissues; influence of the APOL1 variants on the histopathology of HIV kidney disease; possible association with kidney transplant durability; onset of kidney failure at a younger age; association with blood lipid concentrations; more precise geographic localization of individuals with these variants to western and southern African ancestry; and the absence of the variants and kidney disease predisposition in Ethiopians. The definition of APOL1 nephropathy also confirms the long-held assumption by many clinicians that kidney disease attributed to hypertension in African populations represents an underlying glomerulopathy. Still awaited is the delineation of the biologic mechanisms of cellular injury related to these variants, to provide biologic proof of the APOL1 association and to provide potential targets for preventive and therapeutic intervention.

The roles of nearest neighbor methods in imputing missing data in forest inventory and monitoring databases

Treesearch

Bianca N. I. Eskelson; Hailemariam Temesgen; Valerie Lemay; Tara M. Barrett; Nicholas L. Crookston; Andrew T. Hudak

2009-01-01

Almost universally, forest inventory and monitoring databases are incomplete, ranging from missing data for only a few records and a few variables, common for small land areas, to missing data for many observations and many variables, common for large land areas. For a wide variety of applications, nearest neighbor (NN) imputation methods have been developed to fill in...

EPICS Input Output Controller (IOC) Record Reference Manual

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

Anderson, J.B.; Kraimer, M.R.

1994-12-01

This manual describes all supported EPICS record types. The first chapter gives introduction and describes the field summary table. The second chapter describes the fields in database common, i.e. the fields that are present in every record type. The third chapter describes the input and output field that are common to many record types and have the same usage wherever they are used. Following the third chapter is a separate chapter for each record type containing a description of all the fields for that record type except those in database common.

Omics databases on kidney disease: where they can be found and how to benefit from them.

PubMed

Papadopoulos, Theofilos; Krochmal, Magdalena; Cisek, Katryna; Fernandes, Marco; Husi, Holger; Stevens, Robert; Bascands, Jean-Loup; Schanstra, Joost P; Klein, Julie

2016-06-01

In the recent decades, the evolution of omics technologies has led to advances in all biological fields, creating a demand for effective storage, management and exchange of rapidly generated data and research discoveries. To address this need, the development of databases of experimental outputs has become a common part of scientific practice in order to serve as knowledge sources and data-sharing platforms, providing information about genes, transcripts, proteins or metabolites. In this review, we present omics databases available currently, with a special focus on their application in kidney research and possibly in clinical practice. Databases are divided into two categories: general databases with a broad information scope and kidney-specific databases distinctively concentrated on kidney pathologies. In research, databases can be used as a rich source of information about pathophysiological mechanisms and molecular targets. In the future, databases will support clinicians with their decisions, providing better and faster diagnoses and setting the direction towards more preventive, personalized medicine. We also provide a test case demonstrating the potential of biological databases in comparing multi-omics datasets and generating new hypotheses to answer a critical and common diagnostic problem in nephrology practice. In the future, employment of databases combined with data integration and data mining should provide powerful insights into unlocking the mysteries of kidney disease, leading to a potential impact on pharmacological intervention and therapeutic disease management.

A Relational Algebra Query Language for Programming Relational Databases

ERIC Educational Resources Information Center

McMaster, Kirby; Sambasivam, Samuel; Anderson, Nicole

2011-01-01

In this paper, we describe a Relational Algebra Query Language (RAQL) and Relational Algebra Query (RAQ) software product we have developed that allows database instructors to teach relational algebra through programming. Instead of defining query operations using mathematical notation (the approach commonly taken in database textbooks), students…

Academic Journal Embargoes and Full Text Databases.

ERIC Educational Resources Information Center

Brooks, Sam

2003-01-01

Documents the reasons for embargoes of academic journals in full text databases (i.e., publisher-imposed delays on the availability of full text content) and provides insight regarding common misconceptions. Tables present data on selected journals covering a cross-section of subjects and publishers and comparing two full text business databases.…

Structure and needs of global loss databases about natural disaster

NASA Astrophysics Data System (ADS)

Steuer, Markus

2010-05-01

Global loss databases are used for trend analyses and statistics in scientific projects, studies for governmental and nongovernmental organizations and for the insurance and finance industry as well. At the moment three global data sets are established: EM-DAT (CRED), Sigma (Swiss Re) and NatCatSERVICE (Munich Re). Together with the Asian Disaster Reduction Center (ADRC) and United Nations Development Program (UNDP) started a collaborative initiative in 2007 with the aim to agreed on and implemented a common "Disaster Category Classification and Peril Terminology for Operational Databases". This common classification has been established through several technical meetings and working groups and represents a first and important step in the development of a standardized international classification of disasters and terminology of perils. This means concrete to set up a common hierarchy and terminology for all global and regional databases on natural disasters and establish a common and agreed definition of disaster groups, main types and sub-types of events. Also the theme of georeferencing, temporal aspects, methodology and sourcing were other issues that have been identified and will be discussed. The implementation of the new and defined structure for global loss databases is already set up for Munich Re NatCatSERVICE. In the following oral session we will show the structure of the global databases as defined and in addition to give more transparency of the data sets behind published statistics and analyses. The special focus will be on the catastrophe classification from a moderate loss event up to a great natural catastrophe, also to show the quality of sources and give inside information about the assessment of overall and insured losses. Keywords: disaster category classification, peril terminology, overall and insured losses, definition

Listen to your heart: when false somatic feedback shapes moral behavior.

PubMed

Gu, Jun; Zhong, Chen-Bo; Page-Gould, Elizabeth

2013-05-01

A pounding heart is a common symptom people experience when confronting moral dilemmas. The authors conducted 4 experiments using a false feedback paradigm to explore whether and when listening to a fast (vs. normal) heartbeat sound shaped ethical behavior. Study 1 found that perceived fast heartbeat increased volunteering for a just cause. Study 2 extended this effect to moral transgressions and showed that perceived fast heartbeat reduced lying for self-gain. Studies 3 and 4 explored the boundary conditions of this effect and found that perceived heartbeat had less influence on deception when people are mindful or approach the decision deliberatively. These findings suggest that the perceived physiological experience of fast heartbeats may signal greater distress in moral situations and hence motivate people to take the moral high road. PsycINFO Database Record (c) 2013 APA, all rights reserved.

Analysis of single nucleotide polymorphisms in the 3' region of the estrogen receptor 1 gene in normal and cryptorchid Miniature Dachshunds and Chihuahuas.

PubMed

Pathirana, Indunil Nishantha; Tanaka, Kakeru; Kawate, Noritoshi; Tsuji, Makoto; Kida, Kayoko; Hatoya, Shingo; Inaba, Toshio; Tamada, Hiromichi

2010-08-01

This study was performed to examine the distribution of single nucleotide polymorphisms (SNPs) and estimated haplotypes in the canine estrogen receptor (ER) alpha gene (ESR1) and the association of them with different phenotypes of cryptorchidism (CO) in Miniature Dachshunds and Chihuahuas. Forty CO and 68 normal dogs were used, and CO was classified into unilateral (UCO; n=33) and bilateral CO (BCO; n=5) or into abdominal (ACO; n=16) and inguinal CO (ICO; n=22). Thirteen DNA fragments located in the 70-kb region at the 3' end of ESR1 were amplified by PCR and sequenced to examine 13 SNPs (#1-#13) reported in a canine SNP database. Ten SNPs (#1-#4, #7, #8, #10-#13) were not polymorphic, and 5 new SNPs (#14-#18) were discovered. A common haplotype block in normal, CO and CO phenotypes was identified for an approximately 20-kb region encompassing 4 SNPs (#14-#17). Allele, genotype and haplotype frequencies in CO without classification by phenotype and also in UCO, ACO and ICO phenotypes were not statistically different from the normal group. Significant differences in genotype frequencies and homozygosity for the estimated GTTG haplotype within the block were observed in BCO compared with the normal group, although the number of BCO animals was small. Our results demonstrate that the examined SNPs and haplotypes in the 3' end of canine ESR1 are not associated with unilateral, abdominal and inguinal CO phenotypes and CO per se in Miniature Dachshunds and Chihuahuas. Further studies are necessary to suggest a clear association between the ESR1 SNPs and bilateral CO in dogs.

Abnormal plasma sodium concentrations in patients treated with desmopressin for cranial diabetes insipidus: results of a long-term retrospective study.

PubMed

Behan, L A; Sherlock, M; Moyles, P; Renshaw, O; Thompson, C J T; Orr, C; Holte, K; Salehmohamed, M R; Glynn, N; Tormey, W; Thompson, C J

2015-03-01

Patients with cranial diabetes insipidus (CDI) are at risk of developing both hypernatraemia and hyponatraemia, due to the condition itself or secondary to treatment with vasopressin-analogues or during administration of i.v. fluids. We aimed to assess the frequency and impact of dysnatraemias in the inpatient (INPT) and outpatient (OPT) setting in desmopressin-treated CDI, comparing those with normal thirst with those with abnormal thirst. The study included 192 patients with cranial diabetes, who were identified from the Beaumont Pituitary Database, a tertiary referral centre. Retrospective case note audit was performed and the clinical and biochemical information of 147 patients with CDI were available for analysis. A total of 4142 plasma sodium measurements for 137 patients with normal thirst, and 385 plasma sodium measurements for ten patients with abnormal thirst were analysed. In those with normal thirst, the most common OPT abnormality was mild hyponatraemia (pNa(+) 131-134  mmol/l) in 27%, while 14.6% had more significant hyponatraemia (pNa(+) ≤130  mmol/l). Of those patients with normal thirst, 5.8% were admitted due to complications directly related to hyponatraemia. Compared with patients with normal thirst, those with abnormal thirst were more likely to develop significant OPT hypernatraemia (20% vs 1.4%, P=0.02) and significant INPT hyponatraemia (50% vs 11.1%, P 0.02). OPT management of CDI is complicated by a significant incidence of hyponatraemia. In contrast, OPT hypernatraemia is almost exclusively a complication seen in adipsic CDI, who also had more frequent INPT hyponatraemia. CDI associated with thirst disorder requires increased physician attention and patient awareness of potential complications. © 2015 European Society of Endocrinology.

The database of chromosome imbalance regions and genes resided in lung cancer from Asian and Caucasian identified by array-comparative genomic hybridization

PubMed Central

2012-01-01

Background Cancer-related genes show racial differences. Therefore, identification and characterization of DNA copy number alteration regions in different racial groups helps to dissect the mechanism of tumorigenesis. Methods Array-comparative genomic hybridization (array-CGH) was analyzed for DNA copy number profile in 40 Asian and 20 Caucasian lung cancer patients. Three methods including MetaCore analysis for disease and pathway correlations, concordance analysis between array-CGH database and the expression array database, and literature search for copy number variation genes were performed to select novel lung cancer candidate genes. Four candidate oncogenes were validated for DNA copy number and mRNA and protein expression by quantitative polymerase chain reaction (qPCR), chromogenic in situ hybridization (CISH), reverse transcriptase-qPCR (RT-qPCR), and immunohistochemistry (IHC) in more patients. Results We identified 20 chromosomal imbalance regions harboring 459 genes for Caucasian and 17 regions containing 476 genes for Asian lung cancer patients. Seven common chromosomal imbalance regions harboring 117 genes, included gain on 3p13-14, 6p22.1, 9q21.13, 13q14.1, and 17p13.3; and loss on 3p22.2-22.3 and 13q13.3 were found both in Asian and Caucasian patients. Gene validation for four genes including ARHGAP19 (10q24.1) functioning in Rho activity control, FRAT2 (10q24.1) involved in Wnt signaling, PAFAH1B1 (17p13.3) functioning in motility control, and ZNF322A (6p22.1) involved in MAPK signaling was performed using qPCR and RT-qPCR. Mean gene dosage and mRNA expression level of the four candidate genes in tumor tissues were significantly higher than the corresponding normal tissues (P<0.001~P=0.06). In addition, CISH analysis of patients indicated that copy number amplification indeed occurred for ARHGAP19 and ZNF322A genes in lung cancer patients. IHC analysis of paraffin blocks from Asian Caucasian patients demonstrated that the frequency of PAFAH1B1 protein overexpression was 68% in Asian and 70% in Caucasian. Conclusions Our study provides an invaluable database revealing common and differential imbalance regions at specific chromosomes among Asian and Caucasian lung cancer patients. Four validation methods confirmed our database, which would help in further studies on the mechanism of lung tumorigenesis. PMID:22691236

Distinct profiles of expressed sequence tags during intestinal regeneration in the sea cucumber Holothuria glaberrima

PubMed Central

Rojas-Cartagena, Carmencita; Ortíz-Pineda, Pablo; Ramírez-Gómez, Francisco; Suárez-Castillo, Edna C.; Matos-Cruz, Vanessa; Rodríguez, Carlos; Ortíz-Zuazaga, Humberto; García-Arrarás, José E.

2010-01-01

Repair and regeneration are key processes for tissue maintenance, and their disruption may lead to disease states. Little is known about the molecular mechanisms that underline the repair and regeneration of the digestive tract. The sea cucumber Holothuria glaberrima represents an excellent model to dissect and characterize the molecular events during intestinal regeneration. To study the gene expression profile, cDNA libraries were constructed from normal, 3-day, and 7-day regenerating intestines of H. glaberrima. Clones were randomly sequenced and queried against the nonredundant protein database at the National Center for Biotechnology Information. RT-PCR analyses were made of several genes to determine their expression profile during intestinal regeneration. A total of 5,173 sequences from three cDNA libraries were obtained. About 46.2, 35.6, and 26.2% of the sequences for the normal, 3-days, and 7-days cDNA libraries, respectively, shared significant similarity with known sequences in the protein database of GenBank but only present 10% of similarity among them. Analysis of the libraries in terms of functional processes, protein domains, and most common sequences suggests that a differential expression profile is taking place during the regeneration process. Further examination of the expressed sequence tag dataset revealed that 12 putative genes are differentially expressed at significant level (R > 6). Experimental validation by RT-PCR analysis reveals that at least three genes (unknown C-4677-1, melanotransferrin, and centaurin) present a differential expression during regeneration. These findings strongly suggest that the gene expression profile varies among regeneration stages and provide evidence for the existence of differential gene expression. PMID:17579180

Development of Exoplanet database "ExoKyoto" aiming for inter-comparison with different criteria of Habitable zones

NASA Astrophysics Data System (ADS)

Yamashiki, Yosuke; Notsu, Yuta; Sasaki, Takanori; Hosono, Natsuki; Kuroki, Ryusuke; Notsu, Shota; Murashima, Keiya; Takagi, Fuka; Doi, Takao

2017-05-01

An integrated database of confirmed exoplanets has been developed and launched as “ExoKyoto,” for the purpose of better comprehension of exoplanetary systems in different star systems. The HOSTSTAR module of the database includes not only host stars for confirmed exoplanets, but also hundreds of thousands of stars existing in the star database listed in (HYG database). Each hoststar can be referred to in the catalogue with its habitable zone calculated, based on the observed/estimated star parameters. For outreach and observation support purpose, ExoKyoto possesses Stellar Windows, developed by the Xlib & Ggd module, and interfaces with GoogleSky for easy comprehension of those celestial bodies on a stellar map. Target stars can be identified and listed by using this database, based on the target magnitude, transit frequency, and photon decrease ratio by its transit.If we interpolate deficient data using assumed functions about the exoplanets that were discovered until now, Sub-Neptune size (1.9-3.1R_Earth) are the most common (971); then Super Earth size (1.2-1.9 R_earth) have been allocated (681).Using the Solar Equivalent Astronomical Unit (SEAU), most of the exoplanets discovered are within a Venus equivalent orbit (3029), and 197 are located within the habitable zone (Venus to Mars equivalent orbit). If we classify them using Kopparapu et al.(2013), within Recent Venus equivalent orbit (3048), there are 130 located in the habitable zone (runaway greenhouse-maximum greenhouse). For example, Kepler-560b is defined as in the habitable zone by its SEAU, but not by Kopparapu et al. (2013). Furthermore, based on an exoplanet's solar revolution, radius, assumed mass (Larsen & Geoffrey, 2014), transit parameters , and main start information (location, class, spectral class, etc.); observation target selection is practical and possible.In addition to the previous habitable zone based on the normal radiation flux from the host star, we'll discuss stellar flares activities which may disturb planets located in the habitable zone through high energetic particles.*those numbers are in February 2017

A global multiproxy database for temperature reconstructions of the Common Era.

PubMed

2017-07-11

Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850-2014. Global temperature composites show a remarkable degree of coherence between high- and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python.

A global multiproxy database for temperature reconstructions of the Common Era

USGS Publications Warehouse

Emile-Geay, Julian; McKay, Nicholas P.; Kaufman, Darrell S.; von Gunten, Lucien; Wang, Jianghao; Anchukaitis, Kevin J.; Abram, Nerilie J.; Addison, Jason A.; Curran, Mark A.J.; Evans, Michael N.; Henley, Benjamin J.; Hao, Zhixin; Martrat, Belen; McGregor, Helen V.; Neukom, Raphael; Pederson, Gregory T.; Stenni, Barbara; Thirumalai, Kaustubh; Werner, Johannes P.; Xu, Chenxi; Divine, Dmitry V.; Dixon, Bronwyn C.; Gergis, Joelle; Mundo, Ignacio A.; Nakatsuka, T.; Phipps, Steven J.; Routson, Cody C.; Steig, Eric J.; Tierney, Jessica E.; Tyler, Jonathan J.; Allen, Kathryn J.; Bertler, Nancy A. N.; Bjorklund, Jesper; Chase, Brian M.; Chen, Min-Te; Cook, Ed; de Jong, Rixt; DeLong, Kristine L.; Dixon, Daniel A.; Ekaykin, Alexey A.; Ersek, Vasile; Filipsson, Helena L.; Francus, Pierre; Freund, Mandy B.; Frezzotti, M.; Gaire, Narayan P.; Gajewski, Konrad; Ge, Quansheng; Goosse, Hugues; Gornostaeva, Anastasia; Grosjean, Martin; Horiuchi, Kazuho; Hormes, Anne; Husum, Katrine; Isaksson, Elisabeth; Kandasamy, Selvaraj; Kawamura, Kenji; Koc, Nalan; Leduc, Guillaume; Linderholm, Hans W.; Lorrey, Andrew M.; Mikhalenko, Vladimir; Mortyn, P. Graham; Motoyama, Hideaki; Moy, Andrew D.; Mulvaney, Robert; Munz, Philipp M.; Nash, David J.; Oerter, Hans; Opel, Thomas; Orsi, Anais J.; Ovchinnikov, Dmitriy V.; Porter, Trevor J.; Roop, Heidi; Saenger, Casey; Sano, Masaki; Sauchyn, David; Saunders, K.M.; Seidenkrantz, Marit-Solveig; Severi, Mirko; Shao, X.; Sicre, Marie-Alexandrine; Sigl, Michael; Sinclair, Kate; St. George, Scott; St. Jacques, Jeannine-Marie; Thamban, Meloth; Thapa, Udya Kuwar; Thomas, E.; Turney, Chris; Uemura, Ryu; Viau, A.E.; Vladimirova, Diana O.; Wahl, Eugene; White, James W. C.; Yu, Z.; Zinke, Jens

2017-01-01

Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850–2014. Global temperature composites show a remarkable degree of coherence between high- and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python.

A global multiproxy database for temperature reconstructions of the Common Era

PubMed Central

Emile-Geay, Julien; McKay, Nicholas P.; Kaufman, Darrell S.; von Gunten, Lucien; Wang, Jianghao; Anchukaitis, Kevin J.; Abram, Nerilie J.; Addison, Jason A.; Curran, Mark A.J.; Evans, Michael N.; Henley, Benjamin J.; Hao, Zhixin; Martrat, Belen; McGregor, Helen V.; Neukom, Raphael; Pederson, Gregory T.; Stenni, Barbara; Thirumalai, Kaustubh; Werner, Johannes P.; Xu, Chenxi; Divine, Dmitry V.; Dixon, Bronwyn C.; Gergis, Joelle; Mundo, Ignacio A.; Nakatsuka, Takeshi; Phipps, Steven J.; Routson, Cody C.; Steig, Eric J.; Tierney, Jessica E.; Tyler, Jonathan J.; Allen, Kathryn J.; Bertler, Nancy A.N.; Björklund, Jesper; Chase, Brian M.; Chen, Min-Te; Cook, Ed; de Jong, Rixt; DeLong, Kristine L.; Dixon, Daniel A.; Ekaykin, Alexey A.; Ersek, Vasile; Filipsson, Helena L.; Francus, Pierre; Freund, Mandy B.; Frezzotti, Massimo; Gaire, Narayan P.; Gajewski, Konrad; Ge, Quansheng; Goosse, Hugues; Gornostaeva, Anastasia; Grosjean, Martin; Horiuchi, Kazuho; Hormes, Anne; Husum, Katrine; Isaksson, Elisabeth; Kandasamy, Selvaraj; Kawamura, Kenji; Kilbourne, K. Halimeda; Koç, Nalan; Leduc, Guillaume; Linderholm, Hans W.; Lorrey, Andrew M.; Mikhalenko, Vladimir; Mortyn, P. Graham; Motoyama, Hideaki; Moy, Andrew D.; Mulvaney, Robert; Munz, Philipp M.; Nash, David J.; Oerter, Hans; Opel, Thomas; Orsi, Anais J.; Ovchinnikov, Dmitriy V.; Porter, Trevor J.; Roop, Heidi A.; Saenger, Casey; Sano, Masaki; Sauchyn, David; Saunders, Krystyna M.; Seidenkrantz, Marit-Solveig; Severi, Mirko; Shao, Xuemei; Sicre, Marie-Alexandrine; Sigl, Michael; Sinclair, Kate; St. George, Scott; St. Jacques, Jeannine-Marie; Thamban, Meloth; Kuwar Thapa, Udya; Thomas, Elizabeth R.; Turney, Chris; Uemura, Ryu; Viau, Andre E.; Vladimirova, Diana O.; Wahl, Eugene R.; White, James W.C.; Yu, Zicheng; Zinke, Jens

2017-01-01

Reproducible climate reconstructions of the Common Era (1 CE to present) are key to placing industrial-era warming into the context of natural climatic variability. Here we present a community-sourced database of temperature-sensitive proxy records from the PAGES2k initiative. The database gathers 692 records from 648 locations, including all continental regions and major ocean basins. The records are from trees, ice, sediment, corals, speleothems, documentary evidence, and other archives. They range in length from 50 to 2000 years, with a median of 547 years, while temporal resolution ranges from biweekly to centennial. Nearly half of the proxy time series are significantly correlated with HadCRUT4.2 surface temperature over the period 1850–2014. Global temperature composites show a remarkable degree of coherence between high- and low-resolution archives, with broadly similar patterns across archive types, terrestrial versus marine locations, and screening criteria. The database is suited to investigations of global and regional temperature variability over the Common Era, and is shared in the Linked Paleo Data (LiPD) format, including serializations in Matlab, R and Python. PMID:28696409

Toolsets for Airborne Data (TAD): Customized Data Merging Function

NASA Astrophysics Data System (ADS)

Benson, A.; Peeters, M. C.; Perez, J.; Parker, L.; Chen, G.

2013-12-01

NASA has conducted airborne tropospheric chemistry studies for about three decades. These field campaigns have generated a great wealth of observations, including a wide range of the trace gases and aerosol properties. The ASDC Toolset for Airborne Data (TAD) is being designed to meet the user community needs for manipulating aircraft data for scientific research on climate change and air quality relevant issues. Prior to the actual toolset development, a comprehensive metadata database was created to compensate for the absence of standardization of the ICARTT data format in which the data is stored. This database tracks the Principal Investigator-provided metadata, and links the measurement variables to a common naming system that was developed as a part of this project. This database is used by the data merging module. Most aircraft data reported during a single flight is not on a consistent time base and is difficult to intercompare. This module provides the user with the ability to merge original data measurements from multiple data providers into a specified time interval or common time base. The database development, common naming scheme and data merge module development will be presented.

A Tutorial in Creating Web-Enabled Databases with Inmagic DB/TextWorks through ODBC.

ERIC Educational Resources Information Center

Breeding, Marshall

2000-01-01

Explains how to create Web-enabled databases. Highlights include Inmagic's DB/Text WebPublisher product called DB/TextWorks; ODBC (Open Database Connectivity) drivers; Perl programming language; HTML coding; Structured Query Language (SQL); Common Gateway Interface (CGI) programming; and examples of HTML pages and Perl scripts. (LRW)

Rapid identification of anonymous subjects in large criminal databases: problems and solutions in IAFIS III/FBI subject searches

NASA Astrophysics Data System (ADS)

Kutzleb, C. D.

1997-02-01

The high incidence of recidivism (repeat offenders) in the criminal population makes the use of the IAFIS III/FBI criminal database an important tool in law enforcement. The problems and solutions employed by IAFIS III/FBI criminal subject searches are discussed for the following topics: (1) subject search selectivity and reliability; (2) the difficulty and limitations of identifying subjects whose anonymity may be a prime objective; (3) database size, search workload, and search response time; (4) techniques and advantages of normalizing the variability in an individual's name and identifying features into identifiable and discrete categories; and (5) the use of database demographics to estimate the likelihood of a match between a search subject and database subjects.

Personality in general and clinical samples: Measurement invariance of the Multidimensional Personality Questionnaire.

PubMed

Eigenhuis, Annemarie; Kamphuis, Jan H; Noordhof, Arjen

2017-09-01

A growing body of research suggests that the same general dimensions can describe normal and pathological personality, but most of the supporting evidence is exploratory. We aim to determine in a confirmatory framework the extent to which responses on the Multidimensional Personality Questionnaire (MPQ) are identical across general and clinical samples. We tested the Dutch brief form of the MPQ (MPQ-BF-NL) for measurement invariance across a general population subsample (N = 365) and a clinical sample (N = 365), using Multiple Group Confirmatory Factor Analysis (MGCFA) and Multiple Group Exploratory Structural Equation Modeling (MGESEM). As an omnibus personality test, the MPQ-BF-NL revealed strict invariance, indicating absence of bias. Unidimensional per scale tests for measurement invariance revealed that 10% of items appeared to contain bias across samples. Item bias only affected the scale interpretation of Achievement, with individuals from the clinical sample more readily admitting to put high demands on themselves than individuals from the general sample, regardless of trait level. This formal test of equivalence provides strong evidence for the common structure of normal and pathological personality and lends further support to the clinical utility of the MPQ. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

The Human Cell Surfaceome of Breast Tumors

PubMed Central

da Cunha, Júlia Pinheiro Chagas; Galante, Pedro Alexandre Favoretto; de Souza, Jorge Estefano Santana; Pieprzyk, Martin; Carraro, Dirce Maria; Old, Lloyd J.; Camargo, Anamaria Aranha; de Souza, Sandro José

2013-01-01

Introduction. Cell surface proteins are ideal targets for cancer therapy and diagnosis. We have identified a set of more than 3700 genes that code for transmembrane proteins believed to be at human cell surface. Methods. We used a high-throuput qPCR system for the analysis of 573 cell surface protein-coding genes in 12 primary breast tumors, 8 breast cell lines, and 21 normal human tissues including breast. To better understand the role of these genes in breast tumors, we used a series of bioinformatics strategies to integrates different type, of the datasets, such as KEGG, protein-protein interaction databases, ONCOMINE, and data from, literature. Results. We found that at least 77 genes are overexpressed in breast primary tumors while at least 2 of them have also a restricted expression pattern in normal tissues. We found common signaling pathways that may be regulated in breast tumors through the overexpression of these cell surface protein-coding genes. Furthermore, a comparison was made between the genes found in this report and other genes associated with features clinically relevant for breast tumorigenesis. Conclusions. The expression profiling generated in this study, together with an integrative bioinformatics analysis, allowed us to identify putative targets for breast tumors. PMID:24195083

High precision automated face localization in thermal images: oral cancer dataset as test case

NASA Astrophysics Data System (ADS)

Chakraborty, M.; Raman, S. K.; Mukhopadhyay, S.; Patsa, S.; Anjum, N.; Ray, J. G.

2017-02-01

Automated face detection is the pivotal step in computer vision aided facial medical diagnosis and biometrics. This paper presents an automatic, subject adaptive framework for accurate face detection in the long infrared spectrum on our database for oral cancer detection consisting of malignant, precancerous and normal subjects of varied age group. Previous works on oral cancer detection using Digital Infrared Thermal Imaging(DITI) reveals that patients and normal subjects differ significantly in their facial thermal distribution. Therefore, it is a challenging task to formulate a completely adaptive framework to veraciously localize face from such a subject specific modality. Our model consists of first extracting the most probable facial regions by minimum error thresholding followed by ingenious adaptive methods to leverage the horizontal and vertical projections of the segmented thermal image. Additionally, the model incorporates our domain knowledge of exploiting temperature difference between strategic locations of the face. To our best knowledge, this is the pioneering work on detecting faces in thermal facial images comprising both patients and normal subjects. Previous works on face detection have not specifically targeted automated medical diagnosis; face bounding box returned by those algorithms are thus loose and not apt for further medical automation. Our algorithm significantly outperforms contemporary face detection algorithms in terms of commonly used metrics for evaluating face detection accuracy. Since our method has been tested on challenging dataset consisting of both patients and normal subjects of diverse age groups, it can be seamlessly adapted in any DITI guided facial healthcare or biometric applications.

Surgical research using national databases

PubMed Central

Leland, Hyuma; Heckmann, Nathanael

2016-01-01

Recent changes in healthcare and advances in technology have increased the use of large-volume national databases in surgical research. These databases have been used to develop perioperative risk stratification tools, assess postoperative complications, calculate costs, and investigate numerous other topics across multiple surgical specialties. The results of these studies contain variable information but are subject to unique limitations. The use of large-volume national databases is increasing in popularity, and thorough understanding of these databases will allow for a more sophisticated and better educated interpretation of studies that utilize such databases. This review will highlight the composition, strengths, and weaknesses of commonly used national databases in surgical research. PMID:27867945

Surgical research using national databases.

PubMed

Alluri, Ram K; Leland, Hyuma; Heckmann, Nathanael

2016-10-01

Recent changes in healthcare and advances in technology have increased the use of large-volume national databases in surgical research. These databases have been used to develop perioperative risk stratification tools, assess postoperative complications, calculate costs, and investigate numerous other topics across multiple surgical specialties. The results of these studies contain variable information but are subject to unique limitations. The use of large-volume national databases is increasing in popularity, and thorough understanding of these databases will allow for a more sophisticated and better educated interpretation of studies that utilize such databases. This review will highlight the composition, strengths, and weaknesses of commonly used national databases in surgical research.

BioMart Central Portal: an open database network for the biological community

PubMed Central

Guberman, Jonathan M.; Ai, J.; Arnaiz, O.; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J.; Di Génova, A.; Forbes, Simon; Fujisawa, T.; Gadaleta, E.; Goodstein, D. M.; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S.; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R.; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J.; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S.; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B.; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J.; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D. T.; Wong-Erasmus, Marie; Yao, L.; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities. Database URL: http://central.biomart.org. PMID:21930507

77 FR 22322 - Common Formats for Patient Safety Data Collection and Event Reporting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-13

... Safety Databases (NPSD). The Common Formats include two general types of formats, generic and event... Common Formats. The inventory includes many systems from the private sector, including prominent academic...

Analysis of prescription database extracted from standard textbooks of traditional Dai medicine.

PubMed

Zhang, Chuang; Chongsuvivatwong, Virasakdi; Keawpradub, Niwat; Lin, Yanfang

2012-08-29

Traditional Dai Medicine (TDM) is one of the four major ethnomedicine of China. In 2007 a group of experts produced a set of seven Dai medical textbooks on this subject. The first two were selected as the main data source to analyse well recognized prescriptions. To quantify patterns of prescriptions, common ingredients, indications and usages of TDM. A relational database linking the prescriptions, ingredients, herb names, indications, and usages was set up. Frequency of pattern of combination and common ingredients were tabulated. A total of 200 prescriptions and 402 herbs were compiled. Prescriptions based on "wind" disorders, a detoxification theory that most commonly deals with symptoms of digestive system diseases, accounted for over one third of all prescriptions. The major methods of preparations mostly used roots and whole herbs. The information extracted from the relational database may be useful for understanding symptomatic treatments. Antidote and detoxification theory deserves further research.

Acute sensitivity of white sturgeon (Acipenser transmontanus) and rainbow trout (Oncorhynchus mykiss) to copper, cadmium, or zinc in water-only laboratory exposures

PubMed Central

Calfee, Robin D; Little, Edward E; Puglis, Holly J; Scott, Erinn; Brumbaugh, William G; Mebane, Christopher A

2014-01-01

The acute toxicity of cadmium, copper, and zinc to white sturgeon (Acipenser transmontanus) and rainbow trout (Oncorhynchus mykiss) were determined for 7 developmental life stages in flow-through water-only exposures. Metal toxicity varied by species and by life stage. Rainbow trout were more sensitive to cadmium than white sturgeon across all life stages, with median effect concentrations (hardness-normalized EC50s) ranging from 1.47 µg Cd/L to 2.62 µg Cd/L with sensitivity remaining consistent during later stages of development. Rainbow trout at 46 d posthatch (dph) ranked at the 2nd percentile of a compiled database for Cd species sensitivity distribution with an EC50 of 1.46 µg Cd/L and 72 dph sturgeon ranked at the 19th percentile (EC50 of 3.02 µg Cd/L). White sturgeon were more sensitive to copper than rainbow trout in 5 of the 7 life stages tested with biotic ligand model (BLM)-normalized EC50s ranging from 1.51 µg Cu/L to 21.9 µg Cu/L. In turn, rainbow trout at 74 dph and 95 dph were more sensitive to copper than white sturgeon at 72 dph and 89 dph, indicating sturgeon become more tolerant in older life stages, whereas older trout become more sensitive to copper exposure. White sturgeon at 2 dph, 16 dph, and 30 dph ranked in the lower percentiles of a compiled database for copper species sensitivity distribution, ranking at the 3rd (2 dph), 5th (16 dph), and 10th (30 dph) percentiles. White sturgeon were more sensitive to zinc than rainbow trout for 1 out of 7 life stages tested (2 dph with an biotic ligand model–normalized EC50 of 209 µg Zn/L) and ranked in the 1st percentile of a compiled database for zinc species sensitivity distribution. Environ Toxicol Chem 2014;33:2259–2272. © 2014. The Authors. This article is a US government work and, as such, is in the public domain in the United States of America. Environmental Toxicology and Chemistry published byWiley Periodicals, Inc. on behalf of SETAC. This is an open access article under the terms of the Creative Commons Attribution-NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. PMID:25043712

Naval Ship Database: Database Design, Implementation, and Schema

DTIC Science & Technology

2013-09-01

incoming data. The solution allows database users to store and analyze data collected by navy ships in the Royal Canadian Navy ( RCN ). The data...understanding RCN jargon and common practices on a typical RCN vessel. This experience led to the development of several error detection methods to...data to be stored in the database. Mr. Massel has also collected data pertaining to day to day activities on RCN vessels that has been imported into

BloodChIP: a database of comparative genome-wide transcription factor binding profiles in human blood cells.

PubMed

Chacon, Diego; Beck, Dominik; Perera, Dilmi; Wong, Jason W H; Pimanda, John E

2014-01-01

The BloodChIP database (http://www.med.unsw.edu.au/CRCWeb.nsf/page/BloodChIP) supports exploration and visualization of combinatorial transcription factor (TF) binding at a particular locus in human CD34-positive and other normal and leukaemic cells or retrieval of target gene sets for user-defined combinations of TFs across one or more cell types. Increasing numbers of genome-wide TF binding profiles are being added to public repositories, and this trend is likely to continue. For the power of these data sets to be fully harnessed by experimental scientists, there is a need for these data to be placed in context and easily accessible for downstream applications. To this end, we have built a user-friendly database that has at its core the genome-wide binding profiles of seven key haematopoietic TFs in human stem/progenitor cells. These binding profiles are compared with binding profiles in normal differentiated and leukaemic cells. We have integrated these TF binding profiles with chromatin marks and expression data in normal and leukaemic cell fractions. All queries can be exported into external sites to construct TF-gene and protein-protein networks and to evaluate the association of genes with cellular processes and tissue expression.

Evaluation of an Online Instructional Database Accessed by QR Codes to Support Biochemistry Practical Laboratory Classes

ERIC Educational Resources Information Center

Yip, Tor; Melling, Louise; Shaw, Kirsty J.

2016-01-01

An online instructional database containing information on commonly used pieces of laboratory equipment was created. In order to make the database highly accessible and to promote its use, QR codes were utilized. The instructional materials were available anytime and accessed using QR codes located on the equipment itself and within undergraduate…

Common Database Interface for Heterogeneous Software Engineering Tools.

DTIC Science & Technology

1987-12-01

SUB-GROUP Database Management Systems ;Programming(Comuters); 1e 05 Computer Files;Information Transfer;Interfaces; 19. ABSTRACT (Continue on reverse...Air Force Institute of Technology Air University In Partial Fulfillment of the Requirements for the Degree of Master of Science in Information Systems ...Literature ..... 8 System 690 Configuration ......... 8 Database Functionis ............ 14 Software Engineering Environments ... 14 Data Manager

Learning lessons from Natech accidents - the eNATECH accident database

NASA Astrophysics Data System (ADS)

Krausmann, Elisabeth; Girgin, Serkan

2016-04-01

When natural hazards impact industrial facilities that house or process hazardous materials, fires, explosions and toxic releases can occur. This type of accident is commonly referred to as Natech accident. In order to prevent the recurrence of accidents or to better mitigate their consequences, lessons-learned type studies using available accident data are usually carried out. Through post-accident analysis, conclusions can be drawn on the most common damage and failure modes and hazmat release paths, particularly vulnerable storage and process equipment, and the hazardous materials most commonly involved in these types of accidents. These analyses also lend themselves to identifying technical and organisational risk-reduction measures that require improvement or are missing. Industrial accident databases are commonly used for retrieving sets of Natech accident case histories for further analysis. These databases contain accident data from the open literature, government authorities or in-company sources. The quality of reported information is not uniform and exhibits different levels of detail and accuracy. This is due to the difficulty of finding qualified information sources, especially in situations where accident reporting by the industry or by authorities is not compulsory, e.g. when spill quantities are below the reporting threshold. Data collection has then to rely on voluntary record keeping often by non-experts. The level of detail is particularly non-uniform for Natech accident data depending on whether the consequences of the Natech event were major or minor, and whether comprehensive information was available for reporting. In addition to the reporting bias towards high-consequence events, industrial accident databases frequently lack information on the severity of the triggering natural hazard, as well as on failure modes that led to the hazmat release. This makes it difficult to reconstruct the dynamics of the accident and renders the development of equipment vulnerability models linking the natural-hazard severity to the observed damage almost impossible. As a consequence, the European Commission has set up the eNATECH database for the systematic collection of Natech accident data and near misses. The database exhibits the more sophisticated accident representation required to capture the characteristics of Natech events and is publicly accessible at http://enatech.jrc.ec.europa.eu. This presentation outlines the general lessons-learning process, introduces the eNATECH database and its specific structure, and discusses natural-hazard specific lessons learned and features common to Natech accidents triggered by different natural hazards.

SMALL-SCALE AND GLOBAL DYNAMOS AND THE AREA AND FLUX DISTRIBUTIONS OF ACTIVE REGIONS, SUNSPOT GROUPS, AND SUNSPOTS: A MULTI-DATABASE STUDY

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

Muñoz-Jaramillo, Andrés; Windmueller, John C.; Amouzou, Ernest C.

2015-02-10

In this work, we take advantage of 11 different sunspot group, sunspot, and active region databases to characterize the area and flux distributions of photospheric magnetic structures. We find that, when taken separately, different databases are better fitted by different distributions (as has been reported previously in the literature). However, we find that all our databases can be reconciled by the simple application of a proportionality constant, and that, in reality, different databases are sampling different parts of a composite distribution. This composite distribution is made up by linear combination of Weibull and log-normal distributions—where a pure Weibull (log-normal) characterizesmore » the distribution of structures with fluxes below (above) 10{sup 21}Mx (10{sup 22}Mx). Additionally, we demonstrate that the Weibull distribution shows the expected linear behavior of a power-law distribution (when extended to smaller fluxes), making our results compatible with the results of Parnell et al. We propose that this is evidence of two separate mechanisms giving rise to visible structures on the photosphere: one directly connected to the global component of the dynamo (and the generation of bipolar active regions), and the other with the small-scale component of the dynamo (and the fragmentation of magnetic structures due to their interaction with turbulent convection)« less

ECG signal quality during arrhythmia and its application to false alarm reduction.

PubMed

Behar, Joachim; Oster, Julien; Li, Qiao; Clifford, Gari D

2013-06-01

An automated algorithm to assess electrocardiogram (ECG) quality for both normal and abnormal rhythms is presented for false arrhythmia alarm suppression of intensive care unit (ICU) monitors. A particular focus is given to the quality assessment of a wide variety of arrhythmias. Data from three databases were used: the Physionet Challenge 2011 dataset, the MIT-BIH arrhythmia database, and the MIMIC II database. The quality of more than 33 000 single-lead 10 s ECG segments were manually assessed and another 12 000 bad-quality single-lead ECG segments were generated using the Physionet noise stress test database. Signal quality indices (SQIs) were derived from the ECGs segments and used as the inputs to a support vector machine classifier with a Gaussian kernel. This classifier was trained to estimate the quality of an ECG segment. Classification accuracies of up to 99% on the training and test set were obtained for normal sinus rhythm and up to 95% for arrhythmias, although performance varied greatly depending on the type of rhythm. Additionally, the association between 4050 ICU alarms from the MIMIC II database and the signal quality, as evaluated by the classifier, was studied. Results suggest that the SQIs should be rhythm specific and that the classifier should be trained for each rhythm call independently. This would require a substantially increased set of labeled data in order to train an accurate algorithm.

Evaluation of the TRPM2 channel as a biomarker in breast cancer using public databases analysis.

PubMed

Sumoza-Toledo, Adriana; Espinoza-Gabriel, Mario Iván; Montiel-Condado, Dvorak

Breast cancer is one of the most common malignancies affecting women. Recent investigations have revealed a major role of ion channels in cancer. The transient receptor potential melastatin-2 (TRPM2) is a plasma membrane and lysosomal channel with important roles in cell migration and cell death in immune cells and tumor cells. In this study, we investigated the prognostic value of TRPM2 channel in breast cancer, analyzing public databases compiled in Oncomine™ (Thermo Fisher, Ann Arbor, MI) and online Kaplan-Meier Plotter platforms. The results revealed that TRPM2 mRNA overexpression is significant in situ and invasive breast carcinoma compared to normal breast tissue. Furthermore, multi-gene validation using Oncomine™ showed that this channel is coexpressed with proteins related to cellular migration, transformation, and apoptosis. On the other hand, Kaplan-Meier analysis exhibited that low expression of TRPM2 could be used to predict poor outcome in ER- and HER2+ breast carcinoma patients. TRPM2 is a promising biomarker for aggressiveness of breast cancer, and a potential target for the development of new therapies. Copyright © 2016 Hospital Infantil de México Federico Gómez. Publicado por Masson Doyma México S.A. All rights reserved.

Envelopment filter and K-means for the detection of QRS waveforms in electrocardiogram.

PubMed

Merino, Manuel; Gómez, Isabel María; Molina, Alberto J

2015-06-01

The electrocardiogram (ECG) is a well-established technique for determining the electrical activity of the heart and studying its diseases. One of the most common pieces of information that can be read from the ECG is the heart rate (HR) through the detection of its most prominent feature: the QRS complex. This paper describes an offline version and a real-time implementation of a new algorithm to determine QRS localization in the ECG signal based on its envelopment and K-means clustering algorithm. The envelopment is used to obtain a signal with only QRS complexes, deleting P, T, and U waves and baseline wander. Two moving average filters are applied to smooth data. The K-means algorithm classifies data into QRS and non-QRS. The technique is validated using 22 h of ECG data from five Physionet databases. These databases were arbitrarily selected to analyze different morphologies of QRS complexes: three stored data with cardiac pathologies, and two had data with normal heartbeats. The algorithm has a low computational load, with no decision thresholds. Furthermore, it does not require any additional parameter. Sensitivity, positive prediction and accuracy from results are over 99.7%. Copyright © 2015 IPEM. Published by Elsevier Ltd. All rights reserved.

Normalizing suffering: A meta-synthesis of experiences of and perspectives on pain and pain management in nursing homes.

PubMed

Vaismoradi, Mojtaba; Skär, Lisa; Söderberg, Siv; Bondas, Terese E

2016-01-01

Older people who live in nursing homes commonly suffer from pain. Therefore, relieving suffering among older people that stems from pain demands knowledge improvement through an integration of international knowledge. This study aimed to integrate current international findings and strengthen the understanding of older people's experiences of and perspectives on pain and pain management in nursing homes. A meta-synthesis study using Noblit and Hare's interpretative meta-ethnography approach was conducted. Empirical research papers from journals were collected from various databases. The search process and appraisal determined six articles for inclusion. Two studies were conducted in the US and one each in Iceland, Norway, the UK, and Australia. The older people's experiences of pain as well as perspectives on pain management from all involved (older people, their family members, and healthcare staff) were integrated into a theoretical model using three themes of "identity of pain," "recognition of pain," and "response to pain." The metaphor of "normalizing suffering" was devised to illustrate the meaning of pain experiences and pain management in nursing homes. Society's common attitude that pain is unavoidable and therefore acceptable in old age in society-among older people themselves as well as those who are responsible for reporting, acknowledging, and relieving pain-must change. The article emphasizes that pain as a primary source of suffering can be relieved, provided that older people are encouraged to report their pain. In addition, healthcare staff require sufficient training to take a person-centered approach towards assessment and management of pain that considers all elements of pain.

Validation of a for anaerobic bacteria optimized MALDI-TOF MS biotyper database: The ENRIA project.

PubMed

Veloo, A C M; Jean-Pierre, H; Justesen, U S; Morris, T; Urban, E; Wybo, I; Kostrzewa, M; Friedrich, A W

2018-03-12

Within the ENRIA project, several 'expertise laboratories' collaborated in order to optimize the identification of clinical anaerobic isolates by using a widely available platform, the Biotyper Matrix Assisted Laser Desorption Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS). Main Spectral Profiles (MSPs) of well characterized anaerobic strains were added to one of the latest updates of the Biotyper database db6903; (V6 database) for common use. MSPs of anaerobic strains nominated for addition to the Biotyper database are included in this validation. In this study, we validated the optimized database (db5989 [V5 database] + ENRIA MSPs) using 6309 anaerobic isolates. Using the V5 database 71.1% of the isolates could be identified with high confidence, 16.9% with low confidence and 12.0% could not be identified. Including the MSPs added to the V6 database and all MSPs created within the ENRIA project, the amount of strains identified with high confidence increased to 74.8% and 79.2%, respectively. Strains that could not be identified using MALDI-TOF MS decreased to 10.4% and 7.3%, respectively. The observed increase in high confidence identifications differed per genus. For Bilophila wadsworthia, Prevotella spp., gram-positive anaerobic cocci and other less commonly encountered species more strains were identified with higher confidence. A subset of the non-identified strains (42.1%) were identified using 16S rDNA gene sequencing. The obtained identities demonstrated that strains could not be identified either due to the generation of spectra of insufficient quality or due to the fact that no MSP of the encountered species was present in the database. Undoubtedly, the ENRIA project has successfully increased the number of anaerobic isolates that can be identified with high confidence. We therefore recommend further expansion of the database to include less frequently isolated species as this would also allow us to gain valuable insight into the clinical relevance of these less common anaerobic bacteria. Copyright © 2018 The Authors. Published by Elsevier Ltd.. All rights reserved.

Comparison of Left Ventricular Hypertrophy by Electrocardiography and Echocardiography in Children Using Analytics Tool.

PubMed

Tague, Lauren; Wiggs, Justin; Li, Qianxi; McCarter, Robert; Sherwin, Elizabeth; Weinberg, Jacqueline; Sable, Craig

2018-05-17

Left ventricular hypertrophy (LVH) is a common finding on pediatric electrocardiography (ECG) leading to many referrals for echocardiography (echo). This study utilizes a novel analytics tool that combines ECG and echo databases to evaluate ECG as a screening tool for LVH. SQL Server 2012 data warehouse incorporated ECG and echo databases for all patients from a single institution from 2006 to 2016. Customized queries identified patients 0-18 years old with LVH on ECG and an echo performed within 24 h. Using data visualization (Tableau) and analytic (Stata 14) software, ECG and echo findings were compared. Of 437,699 encounters, 4637 met inclusion criteria. ECG had high sensitivity (≥ 90%) but poor specificity (43%), and low positive predictive value (< 20%) for echo abnormalities. ECG performed only 11-22% better than chance (AROC = 0.50). 83% of subjects with LVH on ECG had normal left ventricle (LV) structure and size on echo. African-Americans with LVH were least likely to have an abnormal echo. There was a low correlation between V 6 R on ECG and echo-derived Z score of left ventricle diastolic diameter (r = 0.14) and LV mass index (r = 0.24). The data analytics client was able to mine a database of ECG and echo reports, comparing LVH by ECG and LV measurements and qualitative findings by echo, identifying an abnormal LV by echo in only 17% of cases with LVH on ECG. This novel tool is useful for rapid data mining for both clinical and research endeavors.

Systematic analysis of microarray datasets to identify Parkinson's disease‑associated pathways and genes.

PubMed

Feng, Yinling; Wang, Xuefeng

2017-03-01

In order to investigate commonly disturbed genes and pathways in various brain regions of patients with Parkinson's disease (PD), microarray datasets from previous studies were collected and systematically analyzed. Different normalization methods were applied to microarray datasets from different platforms. A strategy combining gene co‑expression networks and clinical information was adopted, using weighted gene co‑expression network analysis (WGCNA) to screen for commonly disturbed genes in different brain regions of patients with PD. Functional enrichment analysis of commonly disturbed genes was performed using the Database for Annotation, Visualization, and Integrated Discovery (DAVID). Co‑pathway relationships were identified with Pearson's correlation coefficient tests and a hypergeometric distribution‑based test. Common genes in pathway pairs were selected out and regarded as risk genes. A total of 17 microarray datasets from 7 platforms were retained for further analysis. Five gene coexpression modules were identified, containing 9,745, 736, 233, 101 and 93 genes, respectively. One module was significantly correlated with PD samples and thus the 736 genes it contained were considered to be candidate PD‑associated genes. Functional enrichment analysis demonstrated that these genes were implicated in oxidative phosphorylation and PD. A total of 44 pathway pairs and 52 risk genes were revealed, and a risk gene pathway relationship network was constructed. Eight modules were identified and were revealed to be associated with PD, cancers and metabolism. A number of disturbed pathways and risk genes were unveiled in PD, and these findings may help advance understanding of PD pathogenesis.

Variations in data collection methods between national databases affect study results: a comparison of the nationwide inpatient sample and national surgical quality improvement program databases for lumbar spine fusion procedures.

PubMed

Bohl, Daniel D; Russo, Glenn S; Basques, Bryce A; Golinvaux, Nicholas S; Fu, Michael C; Long, William D; Grauer, Jonathan N

2014-12-03

There has been an increasing use of national databases to conduct orthopaedic research. Questions regarding the validity and consistency of these studies have not been fully addressed. The purpose of this study was to test for similarity in reported measures between two national databases commonly used for orthopaedic research. A retrospective cohort study of patients undergoing lumbar spinal fusion procedures during 2009 to 2011 was performed in two national databases: the Nationwide Inpatient Sample and the National Surgical Quality Improvement Program. Demographic characteristics, comorbidities, and inpatient adverse events were directly compared between databases. The total numbers of patients included were 144,098 from the Nationwide Inpatient Sample and 8434 from the National Surgical Quality Improvement Program. There were only small differences in demographic characteristics between the two databases. There were large differences between databases in the rates at which specific comorbidities were documented. Non-morbid obesity was documented at rates of 9.33% in the Nationwide Inpatient Sample and 36.93% in the National Surgical Quality Improvement Program (relative risk, 0.25; p < 0.05). Peripheral vascular disease was documented at rates of 2.35% in the Nationwide Inpatient Sample and 0.60% in the National Surgical Quality Improvement Program (relative risk, 3.89; p < 0.05). Similarly, there were large differences between databases in the rates at which specific inpatient adverse events were documented. Sepsis was documented at rates of 0.38% in the Nationwide Inpatient Sample and 0.81% in the National Surgical Quality Improvement Program (relative risk, 0.47; p < 0.05). Acute kidney injury was documented at rates of 1.79% in the Nationwide Inpatient Sample and 0.21% in the National Surgical Quality Improvement Program (relative risk, 8.54; p < 0.05). As database studies become more prevalent in orthopaedic surgery, authors, reviewers, and readers should view these studies with caution. This study shows that two commonly used databases can identify demographically similar patients undergoing a common orthopaedic procedure; however, the databases document markedly different rates of comorbidities and inpatient adverse events. The differences are likely the result of the very different mechanisms through which the databases collect their comorbidity and adverse event data. Findings highlight concerns regarding the validity of orthopaedic database research. Copyright © 2014 by The Journal of Bone and Joint Surgery, Incorporated.

An Evaluation of Database Solutions to Spatial Object Association

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

Kumar, V S; Kurc, T; Saltz, J

2008-06-24

Object association is a common problem encountered in many applications. Spatial object association, also referred to as crossmatch of spatial datasets, is the problem of identifying and comparing objects in two datasets based on their positions in a common spatial coordinate system--one of the datasets may correspond to a catalog of objects observed over time in a multi-dimensional domain; the other dataset may consist of objects observed in a snapshot of the domain at a time point. The use of database management systems to the solve the object association problem provides portability across different platforms and also greater flexibility. Increasingmore » dataset sizes in today's applications, however, have made object association a data/compute-intensive problem that requires targeted optimizations for efficient execution. In this work, we investigate how database-based crossmatch algorithms can be deployed on different database system architectures and evaluate the deployments to understand the impact of architectural choices on crossmatch performance and associated trade-offs. We investigate the execution of two crossmatch algorithms on (1) a parallel database system with active disk style processing capabilities, (2) a high-throughput network database (MySQL Cluster), and (3) shared-nothing databases with replication. We have conducted our study in the context of a large-scale astronomy application with real use-case scenarios.« less

Identification of Escherichia coli and Trueperella pyogenes isolated from the uterus of dairy cows using routine bacteriological testing and Fourier transform infrared spectroscopy.

PubMed

Jaureguiberry, María; Madoz, Laura Vanina; Giuliodori, Mauricio Javier; Wagener, Karen; Prunner, Isabella; Grunert, Tom; Ehling-Schulz, Monika; Drillich, Marc; de la Sota, Rodolfo Luzbel

2016-11-28

Uterine disorders are common postpartum diseases in dairy cows. In practice, uterine treatment is often based on systemic or locally applied antimicrobials with no previous identification of pathogens. Accurate on-farm diagnostics are not available, and routine testing is time-consuming and cost intensive. An accurate method that could simplify the identification of uterine pathogenic bacteria and improve pathogen-specific treatments could be an important advance to practitioners. The objective of the present study was to evaluate whether a database built with uterine bacteria from European dairy cows could be used to identify bacteria from Argentinean cows by Fourier transformed infrared (FTIR) spectroscopy. Uterine samples from 64 multiparous dairy cows with different types of vaginal discharge (VD) were collected between 5 and 60 days postpartum, analyzed by routine bacteriological testing methods and then re-evaluated by FTIR spectroscopy (n = 27). FTIR spectroscopy identified Escherichia coli in 12 out of 14 samples and Trueperella pyogenes in 8 out of 10 samples. The agreement between the two methods was good with a Kappa coefficient of 0.73. In addition, the likelihood for bacterial growth of common uterine pathogens such as E. coli and T. pyogenes tended to increase with VD score. The odds for a positive result to E. coli or T. pyogenes was 1.88 times higher in cows with fetid VD than in herdmates with clear normal VD. We conclude that the presence of E. coli and T. pyogenes in uterine samples from Argentinean dairy cows can be detected with FTIR with the use of a database built with uterine bacteria from European dairy cows. Future studies are needed to determine if FTIR can be used as an alternative to routine bacteriological testing methods.

Neutropenia in the Newborn

PubMed Central

Maheshwari, Akhil

2013-01-01

PURPOSE OF REVIEW Review normal blood neutrophil concentrations and the clinical approach to neutropenia in the neonatal period. A literature search on neonatal neutropenia was performed using the databases PubMed, EMBASE, and Scopus and the electronic archive of abstracts presented at the annual meetings of the Pediatric Academic Societies. RECENT FINDINGS This review summarizes current knowledge on the causes of neutropenia in premature and critically-ill neonates, focusing on common causes such as maternal hypertension, neonatal sepsis, twin-twin transfusion, alloimmunization, and hemolytic disease. The article provides a rational approach to diagnosis and treatment of neonatal neutropenia, including current evidence on the role of recombinant hematopoietic growth factors. SUMMARY Neutrophil counts should be carefully evaluated in premature and critically-ill neonates. Although neutropenia is usually benign and runs a self-limited course in most neonates, it can be prolonged and constitute a serious deficiency in antimicrobial defense in some infants. PMID:24322487

The bridge between two worlds: psychoanalysis and fMRI.

PubMed

Marini, Stefano; Di Tizio, Laura; Dezi, Sira; Armuzzi, Silvia; Pelaccia, Simona; Valchera, Alessandro; Sepede, Gianna; Girinelli, Gabriella; De Berardis, Domenico; Martinotti, Giovanni; Gambi, Francesco; Di Giannantonio, Massimo

2016-02-01

In recent years, a connection between psychoanalysis and neuroscience has been sought. The meeting point between these two branches is represented by neuropsychoanalysis. The goal of the relationship between psychoanalysis and neuroscience is to test psychoanalytic hypotheses in the human brain, using a scientific method. A literature search was conducted on May 2015. PubMed and Scopus databases were used to find studies for the inclusion in the systematic review. Common results of the studies investigated are represented by a reduction, a modulation, or a normalization of the activation patterns found after the psychoanalytic therapy. New findings in the possible and useful relationship between psychoanalysis and neuroscience could change the modalities of relating to patients for psychoanalysts and the way in which neuroscientists plan their research. Researchers should keep in mind that in any scientific research that has to do with people, neuroscience and a scientific method cannot avoid subjective interpretation.

Significance of white-coat hypertension in older persons with isolated systolic hypertension: a meta-analysis using the International Database on Ambulatory Blood Pressure Monitoring in Relation to Cardiovascular Outcomes population.

PubMed

Franklin, Stanley S; Thijs, Lutgarde; Hansen, Tine W; Li, Yan; Boggia, José; Kikuya, Masahiro; Björklund-Bodegård, Kristina; Ohkubo, Takayoshi; Jeppesen, Jørgen; Torp-Pedersen, Christian; Dolan, Eamon; Kuznetsova, Tatiana; Stolarz-Skrzypek, Katarzyna; Tikhonoff, Valérie; Malyutina, Sofia; Casiglia, Edoardo; Nikitin, Yuri; Lind, Lars; Sandoya, Edgardo; Kawecka-Jaszcz, Kalina; Imai, Yutaka; Wang, Jiguang; Ibsen, Hans; O'Brien, Eoin; Staessen, Jan A

2012-03-01

The significance of white-coat hypertension in older persons with isolated systolic hypertension remains poorly understood. We analyzed subjects from the population-based 11-country International Database on Ambulatory Blood Pressure Monitoring in Relation to Cardiovascular Outcomes database who had daytime ambulatory blood pressure (BP; ABP) and conventional BP (CBP) measurements. After excluding persons with diastolic hypertension by CBP (≥90 mm Hg) or by daytime ABP (≥85 mm Hg), a history of cardiovascular disease, and persons <18 years of age, the present analysis totaled 7295 persons, of whom 1593 had isolated systolic hypertension. During a median follow-up of 10.6 years, there was a total of 655 fatal and nonfatal cardiovascular events. The analyses were stratified by treatment status. In untreated subjects, those with white-coat hypertension (CBP ≥140/<90 mm Hg and ABP <135/<85 mm Hg) and subjects with normal BP (CBP <140/<90 mm Hg and ABP <135/<85 mm Hg) were at similar risk (adjusted hazard rate: 1.17 [95% CI: 0.87-1.57]; P=0.29). Furthermore, in treated subjects with isolated systolic hypertension, the cardiovascular risk was similar in elevated conventional and normal daytime systolic BP as compared with those with normal conventional and normal daytime BPs (adjusted hazard rate: 1.10 [95% CI: 0.79-1.53]; P=0.57). However, both treated isolated systolic hypertension subjects with white-coat hypertension (adjusted hazard rate: 2.00; [95% CI: 1.43-2.79]; P<0.0001) and treated subjects with normal BP (adjusted hazard rate: 1.98 [95% CI: 1.49-2.62]; P<0.0001) were at higher risk as compared with untreated normotensive subjects. In conclusion, subjects with sustained hypertension who have their ABP normalized on antihypertensive therapy but with residual white-coat effect by CBP measurement have an entity that we have termed, "treated normalized hypertension." Therefore, one should be cautious in applying the term "white-coat hypertension" to persons receiving antihypertensive treatment.

The database on transgenic luminescent microorganisms as an instrument of studying a microbial component of closed ecosystems

NASA Astrophysics Data System (ADS)

Boyandin, A. N.; Lankin, Y. P.; Kargatova, T. V.; Popova, L. Y.; Pechurkin, N. S.

Luminescent transgenic microorganisms are widely used for study of microbial communities' functioning including closed ones. Bioluminescence is of high sensitive to effects of different environmental factors. Integration of lux-genes into different metabolic ways allows studying many aspects of microorganisms' life permitting to carry out measurements in situ. There is much information about applications of bioluminescent bacteria in different researches. But for effective using these data their summarizing and accumulation in common source is required. Therefore an information system on characteristics of transgenic microorganisms with cloned lux-genes was created. The database and client software related were developed. A database structure includes information on common characteristics of cloned lux-genes, their sources and properties, on regulation of gene expression in bacterial cells, on dependence of bioluminescence manifestation on biotic, abiotic and anthropogenic environmental factors. The database also can store description of changes in bacterial populations depending on environmental changes. The database created allows storing and using bibliographic information and also links to web sites of world collections of microorganisms. Internet publishing software permitting to open access to the database through the Internet is developed.

[Design of computerised database for clinical and basic management of uveal melanoma].

PubMed

Bande Rodríguez, M F; Santiago Varela, M; Blanco Teijeiro, M J; Mera Yañez, P; Pardo Perez, M; Capeans Tome, C; Piñeiro Ces, A

2012-09-01

The uveal melanoma is the most common primary intraocular tumour in adults. The objective of this work is to show how a computerised database has been formed with specific applications, for clinical and research use, to an extensive group of patients diagnosed with uveal melanoma. For the design of the database a selection of categories, attributes and values was created based on the classifications and parameters given by various authors of articles which have had great relevance in the field of uveal melanoma in recent years. The database has over 250 patient entries with specific information on their clinical history, diagnosis, treatment and progress. It enables us to search any parameter of the entry and make quick and simple statistical studies of them. The database models have been transformed into a basic tool for clinical practice, as they are an efficient way of storing, compiling and selective searching of information. When creating a database it is very important to define a common strategy and the use of a standard language. Copyright © 2011 Sociedad Española de Oftalmología. Published by Elsevier Espana. All rights reserved.

Development of a prototype commonality analysis tool for use in space programs

NASA Technical Reports Server (NTRS)

Yeager, Dorian P.

1988-01-01

A software tool to aid in performing commonality analyses, called Commonality Analysis Problem Solver (CAPS), was designed, and a prototype version (CAPS 1.0) was implemented and tested. The CAPS 1.0 runs in an MS-DOS or IBM PC-DOS environment. The CAPS is designed around a simple input language which provides a natural syntax for the description of feasibility constraints. It provides its users with the ability to load a database representing a set of design items, describe the feasibility constraints on items in that database, and do a comprehensive cost analysis to find the most economical substitution pattern.

The diffusion tensor imaging (DTI) component of the NIH MRI study of normal brain development (PedsDTI).

PubMed

Walker, Lindsay; Chang, Lin-Ching; Nayak, Amritha; Irfanoglu, M Okan; Botteron, Kelly N; McCracken, James; McKinstry, Robert C; Rivkin, Michael J; Wang, Dah-Jyuu; Rumsey, Judith; Pierpaoli, Carlo

2016-01-01

The NIH MRI Study of normal brain development sought to characterize typical brain development in a population of infants, toddlers, children and adolescents/young adults, covering the socio-economic and ethnic diversity of the population of the United States. The study began in 1999 with data collection commencing in 2001 and concluding in 2007. The study was designed with the final goal of providing a controlled-access database; open to qualified researchers and clinicians, which could serve as a powerful tool for elucidating typical brain development and identifying deviations associated with brain-based disorders and diseases, and as a resource for developing computational methods and image processing tools. This paper focuses on the DTI component of the NIH MRI study of normal brain development. In this work, we describe the DTI data acquisition protocols, data processing steps, quality assessment procedures, and data included in the database, along with database access requirements. For more details, visit http://www.pediatricmri.nih.gov. This longitudinal DTI dataset includes raw and processed diffusion data from 498 low resolution (3 mm) DTI datasets from 274 unique subjects, and 193 high resolution (2.5 mm) DTI datasets from 152 unique subjects. Subjects range in age from 10 days (from date of birth) through 22 years. Additionally, a set of age-specific DTI templates are included. This forms one component of the larger NIH MRI study of normal brain development which also includes T1-, T2-, proton density-weighted, and proton magnetic resonance spectroscopy (MRS) imaging data, and demographic, clinical and behavioral data. Published by Elsevier Inc.

Digital hand atlas and computer-aided bone age assessment via the Web

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

1999-07-01

A frequently used assessment method of bone age is atlas matching by a radiological examination of a hand image against a reference set of atlas patterns of normal standards. We are in a process of developing a digital hand atlas with a large standard set of normal hand and wrist images that reflect the skeletal maturity, race and sex difference, and current child development. The digital hand atlas will be used for a computer-aided bone age assessment via Web. We have designed and partially implemented a computer-aided diagnostic (CAD) system for Web-based bone age assessment. The system consists of a digital hand atlas, a relational image database and a Web-based user interface. The digital atlas is based on a large standard set of normal hand an wrist images with extracted bone objects and quantitative features. The image database uses a content- based indexing to organize the hand images and their attributes and present to users in a structured way. The Web-based user interface allows users to interact with the hand image database from browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, will be extracted and compared with patterns from the atlas database to assess the bone age. The relevant reference imags and the final assessment report will be sent back to the user's browser via Web. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. In this paper, we present the system design and Web-based client-server model for computer-assisted bone age assessment and our initial implementation of the digital atlas database.

Drug interaction databases in medical literature: transparency of ownership, funding, classification algorithms, level of documentation, and staff qualifications. A systematic review.

PubMed

Kongsholm, Gertrud Gansmo; Nielsen, Anna Katrine Toft; Damkier, Per

2015-11-01

It is well documented that drug-drug interaction databases (DIDs) differ substantially with respect to classification of drug-drug interactions (DDIs). The aim of this study was to study online available transparency of ownership, funding, information, classifications, staff training, and underlying documentation of the five most commonly used open access English language-based online DIDs and the three most commonly used subscription English language-based online DIDs in the literature. We conducted a systematic literature search to identify the five most commonly used open access and the three most commonly used subscription DIDs in the medical literature. The following parameters were assessed for each of the databases: Ownership, classification of interactions, primary information sources, and staff qualification. We compared the overall proportion of yes/no answers from open access databases and subscription databases by Fisher's exact test-both prior to and after requesting missing information. Among open access DIDs, 20/60 items could be verified from the webpage directly compared to 24/36 for the subscription DIDs (p = 0.0028). Following personal request, these numbers rose to 22/60 and 30/36, respectively (p < 0.0001). For items within the "classification of interaction" domain, proportions were 3/25 versus 11/15 available from the webpage (P = 0.0001) and 3/25 versus 15/15 (p < 0.0001) available upon personal request. Available information on online available transparency of ownership, funding, information, classifications, staff training, and underlying documentation varies substantially among various DIDs. Open access DIDs had a statistically lower score on parameters assessed.

Design considerations, architecture, and use of the Mini-Sentinel distributed data system.

PubMed

Curtis, Lesley H; Weiner, Mark G; Boudreau, Denise M; Cooper, William O; Daniel, Gregory W; Nair, Vinit P; Raebel, Marsha A; Beaulieu, Nicolas U; Rosofsky, Robert; Woodworth, Tiffany S; Brown, Jeffrey S

2012-01-01

We describe the design, implementation, and use of a large, multiorganizational distributed database developed to support the Mini-Sentinel Pilot Program of the US Food and Drug Administration (FDA). As envisioned by the US FDA, this implementation will inform and facilitate the development of an active surveillance system for monitoring the safety of medical products (drugs, biologics, and devices) in the USA. A common data model was designed to address the priorities of the Mini-Sentinel Pilot and to leverage the experience and data of participating organizations and data partners. A review of existing common data models informed the process. Each participating organization designed a process to extract, transform, and load its source data, applying the common data model to create the Mini-Sentinel Distributed Database. Transformed data were characterized and evaluated using a series of programs developed centrally and executed locally by participating organizations. A secure communications portal was designed to facilitate queries of the Mini-Sentinel Distributed Database and transfer of confidential data, analytic tools were developed to facilitate rapid response to common questions, and distributed querying software was implemented to facilitate rapid querying of summary data. As of July 2011, information on 99,260,976 health plan members was included in the Mini-Sentinel Distributed Database. The database includes 316,009,067 person-years of observation time, with members contributing, on average, 27.0 months of observation time. All data partners have successfully executed distributed code and returned findings to the Mini-Sentinel Operations Center. This work demonstrates the feasibility of building a large, multiorganizational distributed data system in which organizations retain possession of their data that are used in an active surveillance system. Copyright © 2012 John Wiley & Sons, Ltd.

Analysis of NASA Common Research Model Dynamic Data

NASA Technical Reports Server (NTRS)

Balakrishna, S.; Acheson, Michael J.

2011-01-01

Recent NASA Common Research Model (CRM) tests at the Langley National Transonic Facility (NTF) and Ames 11-foot Transonic Wind Tunnel (11-foot TWT) have generated an experimental database for CFD code validation. The database consists of force and moment, surface pressures and wideband wing-root dynamic strain/wing Kulite data from continuous sweep pitch polars. The dynamic data sets, acquired at 12,800 Hz sampling rate, are analyzed in this study to evaluate CRM wing buffet onset and potential CRM wing flow separation.

Classification of optical coherence tomography images for diagnosing different ocular diseases

NASA Astrophysics Data System (ADS)

Gholami, Peyman; Sheikh Hassani, Mohsen; Kuppuswamy Parthasarathy, Mohana; Zelek, John S.; Lakshminarayanan, Vasudevan

2018-03-01

Optical Coherence tomography (OCT) images provide several indicators, e.g., the shape and the thickness of different retinal layers, which can be used for various clinical and non-clinical purposes. We propose an automated classification method to identify different ocular diseases, based on the local binary pattern features. The database consists of normal and diseased human eye SD-OCT images. We use a multiphase approach for building our classifier, including preprocessing, Meta learning, and active learning. Pre-processing is applied to the data to handle missing features from images and replace them with the mean or median of the corresponding feature. All the features are run through a Correlation-based Feature Subset Selection algorithm to detect the most informative features and omit the less informative ones. A Meta learning approach is applied to the data, in which a SVM and random forest are combined to obtain a more robust classifier. Active learning is also applied to strengthen our classifier around the decision boundary. The primary experimental results indicate that our method is able to differentiate between the normal and non-normal retina with an area under the ROC curve (AUC) of 98.6% and also to diagnose the three common retina-related diseases, i.e., Age-related Macular Degeneration, Diabetic Retinopathy, and Macular Hole, with an AUC of 100%, 95% and 83.8% respectively. These results indicate a better performance of the proposed method compared to most of the previous works in the literature.

Identifying core herbal treatments for children with asthma: implication from a chinese herbal medicine database in taiwan.

PubMed

Chen, Hsing-Yu; Lin, Yi-Hsuan; Thien, Peck-Foong; Chang, Shih-Chieh; Chen, Yu-Chun; Lo, Su-Shun; Yang, Sien-Hung; Chen, Jiun-Liang

2013-01-01

Asthma is one of the most common allergic respiratory diseases around the world and places great burden on medical payment. Chinese herbal medicine (CHM) is commonly used for Taiwanese children to control diseases. The aim of this study is to analyze the CHM prescriptions for asthmatic children by using a nationwide clinical database. The National Health Insurance Research Database (NHIRD) was used to perform this study. Medical records from 1997 to 2009 with diagnosis with asthma made for children aged 6 to 18 were included into the analysis. Association rule mining and social network analysis were used to analyze the prevalence of single CHM and its combinations. Ma-Xing-Gan-Shi-Tang (MXGST) was the most commonly used herbal formula (HF) (20.2% of all prescriptions), followed by Xiao-Qing-Long-Tang (13.1%) and Xing-Su-San (12.8%). Zhe Bei Mu is the most frequently used single herb (SH) (14.6%), followed by Xing Ren (10.7%). MXGST was commonly used with Zhe Bei Mu (3.5%) and other single herbs capable of dispelling phlegm. Besides, MXGST was the core formula to relieve asthma. Further studies about efficacy and drug safety are needed for the CHM commonly used for asthma based on the result of this study.

Medical conditions among Iraqi refugees in Jordan: data from the United Nations Refugee Assistance Information System

PubMed Central

Carone, Marco; Al-Saedy, Huda; Nyce, Sayre; Ghosn, Jad; Mutuerandu, Timothy; Black, Robert E

2012-01-01

Abstract Objective To determine the range and burden of health services utilization among Iraqi refugees receiving health assistance in Jordan, a country of first asylum. Methods Medical conditions, diagnosed in accordance with the tenth revision of the International classification of diseases, were actively monitored from 1January to 31December 2010 using a pilot centralized database in Jordan called the Refugee Assistance Information System. Findings There were 27 166 medical visits by 7642 Iraqi refugees (mean age: 37.4 years; 49% male; 70% from Baghdad; 6% disabled; 3% with a history of torture). Chronic diseases were common, including essential hypertension (22% of refugees), visual disturbances (12%), joint disorders (11%) and type II diabetes mellitus (11%). The most common reasons for seeking acute care were upper respiratory tract infection (11%), supervision of normal pregnancy (4%) and urinary disorders (3%). The conditions requiring the highest number of visits per refugee were cerebrovascular disease (1.46 visits), senile cataract (1.46) and glaucoma (1.44). Sponsored care included 31 747 referrals or consultations to a specialty service, 18 432 drug dispensations, 2307 laboratory studies and 1090 X-rays. The specialties most commonly required were ophthalmology, dentistry, gynaecology and orthopaedic surgery. Conclusion Iraqi refugees in countries of first asylum and resettlement require targeted health services, health education and sustainable prevention and control strategies for predominantly chronic diseases. PMID:22690034

Short Tandem Repeat DNA Internet Database

National Institute of Standards and Technology Data Gateway

SRD 130 Short Tandem Repeat DNA Internet Database (Web, free access)   Short Tandem Repeat DNA Internet Database is intended to benefit research and application of short tandem repeat DNA markers for human identity testing. Facts and sequence information on each STR system, population data, commonly used multiplex STR systems, PCR primers and conditions, and a review of various technologies for analysis of STR alleles have been included.

USE OF EXISTING DATABASES FOR THE PURPOSE OF HAZARD IDENTIFICATION: AN EXAMPLE

EPA Science Inventory

Keywords: existing databases, hazard identification, cancer mortality, birth malformations

Background: Associations between adverse health effects and environmental exposures are difficult to study, because exposures may be widespread, low-dose in nature, and common thro...

Liverome: a curated database of liver cancer-related gene signatures with self-contained context information.

PubMed

Lee, Langho; Wang, Kai; Li, Gang; Xie, Zhi; Wang, Yuli; Xu, Jiangchun; Sun, Shaoxian; Pocalyko, David; Bhak, Jong; Kim, Chulhong; Lee, Kee-Ho; Jang, Ye Jin; Yeom, Young Il; Yoo, Hyang-Sook; Hwang, Seungwoo

2011-11-30

Hepatocellular carcinoma (HCC) is the fifth most common cancer worldwide. A number of molecular profiling studies have investigated the changes in gene and protein expression that are associated with various clinicopathological characteristics of HCC and generated a wealth of scattered information, usually in the form of gene signature tables. A database of the published HCC gene signatures would be useful to liver cancer researchers seeking to retrieve existing differential expression information on a candidate gene and to make comparisons between signatures for prioritization of common genes. A challenge in constructing such database is that a direct import of the signatures as appeared in articles would lead to a loss or ambiguity of their context information that is essential for a correct biological interpretation of a gene's expression change. This challenge arises because designation of compared sample groups is most often abbreviated, ad hoc, or even missing from published signature tables. Without manual curation, the context information becomes lost, leading to uninformative database contents. Although several databases of gene signatures are available, none of them contains informative form of signatures nor shows comprehensive coverage on liver cancer. Thus we constructed Liverome, a curated database of liver cancer-related gene signatures with self-contained context information. Liverome's data coverage is more than three times larger than any other signature database, consisting of 143 signatures taken from 98 HCC studies, mostly microarray and proteome, and involving 6,927 genes. The signatures were post-processed into an informative and uniform representation and annotated with an itemized summary so that all context information is unambiguously self-contained within the database. The signatures were further informatively named and meaningfully organized according to ten functional categories for guided browsing. Its web interface enables a straightforward retrieval of known differential expression information on a query gene and a comparison of signatures to prioritize common genes. The utility of Liverome-collected data is shown by case studies in which useful biological insights on HCC are produced. Liverome database provides a comprehensive collection of well-curated HCC gene signatures and straightforward interfaces for gene search and signature comparison as well. Liverome is available at http://liverome.kobic.re.kr.

Advanced Neuropsychological Diagnostics Infrastructure (ANDI): A Normative Database Created from Control Datasets

PubMed Central

de Vent, Nathalie R.; Agelink van Rentergem, Joost A.; Schmand, Ben A.; Murre, Jaap M. J.; Huizenga, Hilde M.

2016-01-01

In the Advanced Neuropsychological Diagnostics Infrastructure (ANDI), datasets of several research groups are combined into a single database, containing scores on neuropsychological tests from healthy participants. For most popular neuropsychological tests the quantity, and range of these data surpasses that of traditional normative data, thereby enabling more accurate neuropsychological assessment. Because of the unique structure of the database, it facilitates normative comparison methods that were not feasible before, in particular those in which entire profiles of scores are evaluated. In this article, we describe the steps that were necessary to combine the separate datasets into a single database. These steps involve matching variables from multiple datasets, removing outlying values, determining the influence of demographic variables, and finding appropriate transformations to normality. Also, a brief description of the current contents of the ANDI database is given. PMID:27812340

Advanced Neuropsychological Diagnostics Infrastructure (ANDI): A Normative Database Created from Control Datasets.

PubMed

de Vent, Nathalie R; Agelink van Rentergem, Joost A; Schmand, Ben A; Murre, Jaap M J; Huizenga, Hilde M

2016-01-01

In the Advanced Neuropsychological Diagnostics Infrastructure (ANDI), datasets of several research groups are combined into a single database, containing scores on neuropsychological tests from healthy participants. For most popular neuropsychological tests the quantity, and range of these data surpasses that of traditional normative data, thereby enabling more accurate neuropsychological assessment. Because of the unique structure of the database, it facilitates normative comparison methods that were not feasible before, in particular those in which entire profiles of scores are evaluated. In this article, we describe the steps that were necessary to combine the separate datasets into a single database. These steps involve matching variables from multiple datasets, removing outlying values, determining the influence of demographic variables, and finding appropriate transformations to normality. Also, a brief description of the current contents of the ANDI database is given.

PAGE-1, an X chromosome-linked GAGE-like gene that is expressed in normal and neoplastic prostate, testis, and uterus

PubMed Central

Brinkmann, Ulrich; Vasmatzis, George; Lee, Byungkook; Yerushalmi, Noga; Essand, Magnus; Pastan, Ira

1998-01-01

We have used a combination of computerized database mining and experimental expression analyses to identify a gene that is preferentially expressed in normal male and female reproductive tissues, prostate, testis, fallopian tube, uterus, and placenta, as well as in prostate cancer, testicular cancer, and uterine cancer. This gene is located on the human X chromosome, and it is homologous to a family of genes encoding GAGE-like proteins. GAGE proteins are expressed in a variety of tumors and in testis. We designate the novel gene PAGE-1 because the expression pattern in the Cancer Genome Anatomy Project libraries indicates that it is predominantly expressed in normal and neoplastic prostate. Further database analysis indicates the presence of other genes with high homology to PAGE-1, which were found in cDNA libraries derived from testis, pooled libraries (with testis), and in a germ cell tumor library. The expression of PAGE-1 in normal and malignant prostate, testicular, and uterine tissues makes it a possible target for the diagnosis and possibly for the vaccine-based therapy of neoplasms of prostate, testis, and uterus. PMID:9724777

PAGE-1, an X chromosome-linked GAGE-like gene that is expressed in normal and neoplastic prostate, testis, and uterus.

PubMed

Brinkmann, U; Vasmatzis, G; Lee, B; Yerushalmi, N; Essand, M; Pastan, I

1998-09-01

We have used a combination of computerized database mining and experimental expression analyses to identify a gene that is preferentially expressed in normal male and female reproductive tissues, prostate, testis, fallopian tube, uterus, and placenta, as well as in prostate cancer, testicular cancer, and uterine cancer. This gene is located on the human X chromosome, and it is homologous to a family of genes encoding GAGE-like proteins. GAGE proteins are expressed in a variety of tumors and in testis. We designate the novel gene PAGE-1 because the expression pattern in the Cancer Genome Anatomy Project libraries indicates that it is predominantly expressed in normal and neoplastic prostate. Further database analysis indicates the presence of other genes with high homology to PAGE-1, which were found in cDNA libraries derived from testis, pooled libraries (with testis), and in a germ cell tumor library. The expression of PAGE-1 in normal and malignant prostate, testicular, and uterine tissues makes it a possible target for the diagnosis and possibly for the vaccine-based therapy of neoplasms of prostate, testis, and uterus.

Analysis of prescription database extracted from standard textbooks of traditional Dai medicine

PubMed Central

2012-01-01

Background Traditional Dai Medicine (TDM) is one of the four major ethnomedicine of China. In 2007 a group of experts produced a set of seven Dai medical textbooks on this subject. The first two were selected as the main data source to analyse well recognized prescriptions. Objective To quantify patterns of prescriptions, common ingredients, indications and usages of TDM. Methods A relational database linking the prescriptions, ingredients, herb names, indications, and usages was set up. Frequency of pattern of combination and common ingredients were tabulated. Results A total of 200 prescriptions and 402 herbs were compiled. Prescriptions based on "wind" disorders, a detoxification theory that most commonly deals with symptoms of digestive system diseases, accounted for over one third of all prescriptions. The major methods of preparations mostly used roots and whole herbs. Conclusion The information extracted from the relational database may be useful for understanding symptomatic treatments. Antidote and detoxification theory deserves further research. PMID:22931752

Normative database of donor keratographic readings in an eye-bank setting.

PubMed

Lewis, Jennifer R; Bogucki, Jennifer M; Mahmoud, Ashraf M; Lembach, Richard G; Roberts, Cynthia J

2010-04-01

To generate a normative donor topographic database from rasterstereography images of whole globes acquired in an eye-bank setting with minimal manipulation or handling. Eye-bank laboratory. In a retrospective study, rasterstereography topographic images that had been prospectively collected in duplicate of donor eyes received by the Central Ohio Lions Eye Bank between 1997 and 1999 were analyzed. Best-fit sphere (BFS) and simulated keratometry (K) values were extracted. These values were recalculated after application of custom software to correct any tilt of the mapped surfaces relative to the image plane. The mean value variances between right eyes and left eyes, between consecutive scans, and after untilting were analyzed by repeated-measures analysis of variance and t tests (P.05, Kolmogorov-Smirnov). There was no difference between right and left eyes or consecutive scans (P>.05). The mean values changed when the images were tilt-corrected (P<.05). The right eye BFS, Kflat, and Ksteep values of 42.03 diopters (D) +/- 1.88 (SD), 42.21 +/- 2.10 D, and 43.82 +/- 2.00 D, respectively, increased to 42.52 +/- 1.73 D, 43.05 +/- 1.99 D, and 44.57 +/- 2.02 D, respectively, after tilt correction. Keratometric parameter frequency distributions from the donor database of tilt-corrected data were normal in distribution and comparable to parameters reported for normal eyes in a living population. These findings show the feasibility and reliability of routine donor-eye topography by rasterstereography. No author has a financial or proprietary interest in any material or method mentioned. Additional disclosures are found in the footnotes. Copyright (c) 2010 ASCRS and ESCRS. Published by Elsevier Inc. All rights reserved.

Transcriptome changes induced in vitro by alcohol-containing mouthwashes in normal and dysplastic oral keratinocytes.

PubMed

Fox, Simon A; Currie, Sean S; Dalley, Andrew J; Farah, Camile S

2018-05-01

The role of alcohol-containing mouthwash as a risk factor for the development of oral cancer is a subject of conflicting epidemiological evidence in the literature despite alcohol being a recognised carcinogen. The aim of this study was to use in vitro models to investigate mechanistic and global gene expression effects of exposure to alcohol-containing mouthwash. Two brands of alcohol-containing mouthwash and their alcohol-free counterparts were used to treat two oral cell lines derived from normal (OKF6-TERT) and dysplastic (DOK) tissues. Genotoxicity was determined by Comet assay. RNA-seq was performed using the Ion Torrent platform. Bioinformatics analysis used R/Bioconductor packages with differential expression using DEseq2. Pathway enrichment analysis used EnrichR with the WikiPathways and Kegg databases. Both cell lines displayed dose-dependent DNA damage in response to acute exposure to ethanol and alcohol-containing mouthwashes as well as alcohol-free mouthwashes reconstituted with ethanol as shown by Comet assay. The transcriptomic effects of alcohol-containing mouthwash exposure were more complex with significant differential gene expression ranging from >2000 genes in dysplastic (DOK) cells to <100 genes in normal (OKF6-TERT) cells. Pathway enrichment analysis in DOK cells revealed alcohol-containing mouthwashes showed common features between the two brands used including DNA damage response as well as cancer-associated pathways. In OKF6-TERT cells, the most significantly enriched pathways involved inflammatory signalling. Alcohol-containing mouthwashes are genotoxic in vitro to normal and dysplastic oral keratinocytes and induce widespread changes in gene expression. Dysplastic cells are more susceptible to the transcriptomic effects of mouthwash. © 2018 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Reference values of MRI measurements of the common bile duct and pancreatic duct in children.

PubMed

Gwal, Kriti; Bedoya, Maria A; Patel, Neal; Rambhatla, Siri J; Darge, Kassa; Sreedharan, Ram R; Anupindi, Sudha A

2015-07-01

Magnetic resonance imaging/cholangiopancreatography (MRI/MRCP) is now an essential imaging modality for the evaluation of biliary and pancreatic pathology in children, but there are no data depicting the normal diameters of the common bile duct (CBD) and pancreatic duct. Recognition of abnormal duct size is important and the increasing use of MRCP necessitates normal MRI measurements. To present normal MRI measurements for the common bile duct and pancreatic duct in children. In this retrospective study we searched all children ages birth to 10 years in our MR urography (MRU) database from 2006 until 2013. We excluded children with a history of hepatobiliary or pancreatic surgery. We stratified 204 children into five age groups and retrospectively measured the CBD and the pancreatic duct on 2-D axial and 3-D coronal T2-weighted sequences. We performed statistical analysis, using logistic and linear regressions to detect the age association of the visibility and size of the duct measurements. We used non-parametric tests to detect gender and imaging plane differences. Our study included 204 children, 106 (52%) boys and 98 (48%) girls, with a median age of 33 months (range 0-119 months). The children were distributed into five age groups. The common bile duct was visible in all children in all age groups. The pancreatic duct was significantly less visible in the youngest children, group 1 (54/67, 80.5%; P = 0.003) than in the oldest children, group 5 (22/22, 100%). In group 2 the pancreatic duct was seen in 19/21 (90.4%), in group 3 52/55 (94.5%), and in group 4 39/39 (100%). All duct measurements increased with age (P < 0.001; r-value > 0.423), and the incremental differences between ages were significant. The measurement variations between the axial and coronal planes were statistically significant (P < 0.001); however these differences were fractions of millimeters. For example, in group 1 the mean coronal measurement of the CBD was 2.1 mm and the axial measurement was 2.0 mm; the mean coronal measurement of the pancreatic duct was 0.9 mm and the axial measurement was 0.8 mm. Our study provides normative measurements for the common bile duct and pancreatic duct for children up to age 10 years. The upper limits of the CBD and pancreatic duct increase with age, and the values range 1.1-4.0 mm for the CBD and 0.6-1.9 mm for the pancreatic duct.

Automatic detection of ECG cable interchange by analyzing both morphology and interlead relations.

PubMed

Han, Chengzong; Gregg, Richard E; Feild, Dirk Q; Babaeizadeh, Saeed

2014-01-01

ECG cable interchange can generate erroneous diagnoses. For algorithms detecting ECG cable interchange, high specificity is required to maintain a low total false positive rate because the prevalence of interchange is low. In this study, we propose and evaluate an improved algorithm for automatic detection and classification of ECG cable interchange. The algorithm was developed by using both ECG morphology information and redundancy information. ECG morphology features included QRS-T and P-wave amplitude, frontal axis and clockwise vector loop rotation. The redundancy features were derived based on the EASI™ lead system transformation. The classification was implemented using linear support vector machine. The development database came from multiple sources including both normal subjects and cardiac patients. An independent database was used to test the algorithm performance. Common cable interchanges were simulated by swapping either limb cables or precordial cables. For the whole validation database, the overall sensitivity and specificity for detecting precordial cable interchange were 56.5% and 99.9%, and the sensitivity and specificity for detecting limb cable interchange (excluding left arm-left leg interchange) were 93.8% and 99.9%. Defining precordial cable interchange or limb cable interchange as a single positive event, the total false positive rate was 0.7%. When the algorithm was designed for higher sensitivity, the sensitivity for detecting precordial cable interchange increased to 74.6% and the total false positive rate increased to 2.7%, while the sensitivity for detecting limb cable interchange was maintained at 93.8%. The low total false positive rate was maintained at 0.6% for the more abnormal subset of the validation database including only hypertrophy and infarction patients. The proposed algorithm can detect and classify ECG cable interchanges with high specificity and low total false positive rate, at the cost of decreased sensitivity for certain precordial cable interchanges. The algorithm could also be configured for higher sensitivity for different applications where a lower specificity can be tolerated. Copyright © 2014 Elsevier Inc. All rights reserved.

What is normal? Female lower limb kinematic profiles during athletic tasks used to examine anterior cruciate ligament injury risk: a systematic review.

PubMed

Fox, Aaron S; Bonacci, Jason; McLean, Scott G; Spittle, Michael; Saunders, Natalie

2014-06-01

It has been proposed that the performance of athletic tasks where normal motion is exceeded has the potential to damage the anterior cruciate ligament (ACL). Determining the expected or 'normal' kinematic profile of athletic tasks commonly used to assess ACL injury risk can provide an evidence base for the identification of abnormal or anomalous task performances in a laboratory setting. The objective was to conduct a systematic review of studies examining lower limb kinematics of females during drop landing, drop vertical jump, and side-step cutting tasks, to determine 'normal' ranges for hip and knee joint kinematic variables. An electronic database search was conducted on the SPORTDiscus(TM), MEDLINE, AMED and CINAHL (January 1980-August 2013) databases using a combination of relevant keywords. Studies identified as potentially relevant were independently examined by two reviewers for inclusion. Where consensus could not be reached, a third reviewer was consulted. Original research articles that examined three-dimensional hip and knee kinematics of female subjects during the athletic tasks of interest were included for review. Articles were excluded if subjects had a history of lower back or lower limb joint injury or isolated data from the female cohort could not be extracted. Two reviewers independently assessed the quality of included studies. Data on subject characteristics, the athletic task performed, and kinematic data were extracted from included studies. Studies were categorised according to the athletic task being examined and each study allocated a weight within categories based on the number of subjects assessed. Extracted data were used to calculate the weighted means and standard deviations for hip and knee kinematics (initial contact and peak values). 'Normal' motion was classified as the weighted mean plus/minus one standard deviation. Of 2,920 citations, a total of 159 articles were identified as potentially relevant, with 29 meeting all inclusion/exclusion criteria. Due to the limited number of studies available examining double-leg drop landings and single-leg drop vertical jumps, insufficient data was available to include these tasks in the review. Therefore, a total of 25 articles were included. From the included studies, 'normal' ranges were calculated for the kinematic variables of interest across the athletic tasks examined. Joint forces and other additional elements play a role in ACL injuries, therefore, focusing solely on lower limb kinematics in classifying injury risk may not encapsulate all relevant factors. Insufficient data resulted in no normal ranges being calculated for double-leg drop land and single-leg drop vertical jump tasks. No included study examined hip internal/external rotation during single-leg drop landings, therefore ranges for this kinematic variable could not be determined. Variation in data between studies resulted in wide normal ranges being observed across certain kinematic variables. The ranges calculated in this review provide evidence-based values that can be used to identify abnormal or anomalous athletic task performances on a multi-planar scale. This may be useful in identifying neuromuscular factors or specific muscular recruitment strategies that contribute to ACL injury risk.

23 CFR 973.204 - Management systems requirements.

Code of Federal Regulations, 2012 CFR

2012-04-01

... Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION FEDERAL LANDS HIGHWAYS MANAGEMENT... system; (2) A process to operate and maintain the management systems and their associated databases; (3... systems shall use databases with a common or coordinated reference system that can be used to geolocate...

23 CFR 973.204 - Management systems requirements.

Code of Federal Regulations, 2011 CFR

2011-04-01

... Highways FEDERAL HIGHWAY ADMINISTRATION, DEPARTMENT OF TRANSPORTATION FEDERAL LANDS HIGHWAYS MANAGEMENT... system; (2) A process to operate and maintain the management systems and their associated databases; (3... systems shall use databases with a common or coordinated reference system that can be used to geolocate...

Acupuncture for common cold: A systematic review and meta-analyze protocol.

PubMed

Cheng, Ying; Gao, Bifeng; Jin, Yuhao; Xu, Na; Guo, Taipin

2018-03-01

The common cold (CC) is the most common syndromes of infection in human beings, but there is currently no special treatment. For this reason, acupuncture is used to relieve the symptoms of the CC. Acupuncture is a traditional Chinese medicine (TCM) therapy that has been used for over 2000 years to treat various diseases. However, few studies have provided evidence for the efficacy and safety of acupuncture for the CC. This study aims to evaluate the effectiveness and safety of acupuncture on CC periods and its symptoms. The following electronic databases will be searched for studies conducted through January 1, 2019: Web of Science, Cochrane Library, EBASE, World Health Organization International Clinical Trials Registry Platform, Springer, Wan-fang database, Chinese Biomedical Literature Database (CBM), Chinese Scientific Journal Database (VIP), China National Knowledge Infrastructure (CNKI), and other sources. All randomized controlled trials on acupuncture for common cold will be included. Risk of bias will be assessed using the Cochrane risk of bias assessment tool, while RevMan V.5.3.5 software will be implemented for the assessment of bias risk, data synthesis, subgroup analysis, and meta-analyses if conditions are met. Continuous outcomes will be presented as mean difference (MD) or standard mean difference (SMD), while dichotomous data will be expressed as relative risk. A high-quality synthesis of current evidence of acupuncture for CC will be stated from several aspect using subjective reports and objective measures of performance. The reduction rate of common cold symptoms after initial treatment, resolved cold symptoms, and reduced cold duration will be collected. This protocol will present the evidence of whether acupuncture therapy is an effective intervention for CC.

New methods in iris recognition.

PubMed

Daugman, John

2007-10-01

This paper presents the following four advances in iris recognition: 1) more disciplined methods for detecting and faithfully modeling the iris inner and outer boundaries with active contours, leading to more flexible embedded coordinate systems; 2) Fourier-based methods for solving problems in iris trigonometry and projective geometry, allowing off-axis gaze to be handled by detecting it and "rotating" the eye into orthographic perspective; 3) statistical inference methods for detecting and excluding eyelashes; and 4) exploration of score normalizations, depending on the amount of iris data that is available in images and the required scale of database search. Statistical results are presented based on 200 billion iris cross-comparisons that were generated from 632500 irises in the United Arab Emirates database to analyze the normalization issues raised in different regions of receiver operating characteristic curves.

TMC-SNPdb: an Indian germline variant database derived from whole exome sequences.

PubMed

Upadhyay, Pawan; Gardi, Nilesh; Desai, Sanket; Sahoo, Bikram; Singh, Ankita; Togar, Trupti; Iyer, Prajish; Prasad, Ratnam; Chandrani, Pratik; Gupta, Sudeep; Dutt, Amit

2016-01-01

Cancer is predominantly a somatic disease. A mutant allele present in a cancer cell genome is considered somatic when it's absent in the paired normal genome along with public SNP databases. The current build of dbSNP, the most comprehensive public SNP database, however inadequately represents several non-European Caucasian populations, posing a limitation in cancer genomic analyses of data from these populations. We present the T: ata M: emorial C: entre-SNP D: ata B: ase (TMC-SNPdb), as the first open source, flexible, upgradable, and freely available SNP database (accessible through dbSNP build 149 and ANNOVAR)-representing 114 309 unique germline variants-generated from whole exome data of 62 normal samples derived from cancer patients of Indian origin. The TMC-SNPdb is presented with a companion subtraction tool that can be executed with command line option or using an easy-to-use graphical user interface with the ability to deplete additional Indian population specific SNPs over and above dbSNP and 1000 Genomes databases. Using an institutional generated whole exome data set of 132 samples of Indian origin, we demonstrate that TMC-SNPdb could deplete 42, 33 and 28% false positive somatic events post dbSNP depletion in Indian origin tongue, gallbladder, and cervical cancer samples, respectively. Beyond cancer somatic analyses, we anticipate utility of the TMC-SNPdb in several Mendelian germline diseases. In addition to dbSNP build 149 and ANNOVAR, the TMC-SNPdb along with the subtraction tool is available for download in the public domain at the following:Database URL: http://www.actrec.gov.in/pi-webpages/AmitDutt/TMCSNP/TMCSNPdp.html. © The Author(s) 2016. Published by Oxford University Press.

Ultrasound versus liver function tests for diagnosis of common bile duct stones.

PubMed

Gurusamy, Kurinchi Selvan; Giljaca, Vanja; Takwoingi, Yemisi; Higgie, David; Poropat, Goran; Štimac, Davor; Davidson, Brian R

2015-02-26

Ultrasound and liver function tests (serum bilirubin and serum alkaline phosphatase) are used as screening tests for the diagnosis of common bile duct stones in people suspected of having common bile duct stones. There has been no systematic review of the diagnostic accuracy of ultrasound and liver function tests. To determine and compare the accuracy of ultrasound versus liver function tests for the diagnosis of common bile duct stones. We searched MEDLINE, EMBASE, Science Citation Index Expanded, BIOSIS, and Clinicaltrials.gov to September 2012. We searched the references of included studies to identify further studies and systematic reviews identified from various databases (Database of Abstracts of Reviews of Effects, Health Technology Assessment, Medion, and ARIF (Aggressive Research Intelligence Facility)). We did not restrict studies based on language or publication status, or whether data were collected prospectively or retrospectively. We included studies that provided the number of true positives, false positives, false negatives, and true negatives for ultrasound, serum bilirubin, or serum alkaline phosphatase. We only accepted studies that confirmed the presence of common bile duct stones by extraction of the stones (irrespective of whether this was done by surgical or endoscopic methods) for a positive test result, and absence of common bile duct stones by surgical or endoscopic negative exploration of the common bile duct, or symptom-free follow-up for at least six months for a negative test result as the reference standard in people suspected of having common bile duct stones. We included participants with or without prior diagnosis of cholelithiasis; with or without symptoms and complications of common bile duct stones, with or without prior treatment for common bile duct stones; and before or after cholecystectomy. At least two authors screened abstracts and selected studies for inclusion independently. Two authors independently collected data from each study. Where meta-analysis was possible, we used the bivariate model to summarise sensitivity and specificity. Five studies including 523 participants reported the diagnostic accuracy of ultrasound. One studies (262 participants) compared the accuracy of ultrasound, serum bilirubin and serum alkaline phosphatase in the same participants. All the studies included people with symptoms. One study included only participants without previous cholecystectomy but this information was not available from the remaining studies. All the studies were of poor methodological quality. The sensitivities for ultrasound ranged from 0.32 to 1.00, and the specificities ranged from 0.77 to 0.97. The summary sensitivity was 0.73 (95% CI 0.44 to 0.90) and the specificity was 0.91 (95% CI 0.84 to 0.95). At the median pre-test probability of common bile duct stones of 0.408, the post-test probability (95% CI) associated with positive ultrasound tests was 0.85 (95% CI 0.75 to 0.91), and negative ultrasound tests was 0.17 (95% CI 0.08 to 0.33).The single study of liver function tests reported diagnostic accuracy at two cut-offs for bilirubin (greater than 22.23 μmol/L and greater than twice the normal limit) and two cut-offs for alkaline phosphatase (greater than 125 IU/L and greater than twice the normal limit). This study also assessed ultrasound and reported higher sensitivities for bilirubin and alkaline phosphatase at both cut-offs but the specificities of the markers were higher at only the greater than twice the normal limit cut-off. The sensitivity for ultrasound was 0.32 (95% CI 0.15 to 0.54), bilirubin (cut-off greater than 22.23 μmol/L) was 0.84 (95% CI 0.64 to 0.95), and alkaline phosphatase (cut-off greater than 125 IU/L) was 0.92 (95% CI 0.74 to 0.99). The specificity for ultrasound was 0.95 (95% CI 0.91 to 0.97), bilirubin (cut-off greater than 22.23 μmol/L) was 0.91 (95% CI 0.86 to 0.94), and alkaline phosphatase (cut-off greater than 125 IU/L) was 0.79 (95% CI 0.74 to 0.84). No study reported the diagnostic accuracy of a combination of bilirubin and alkaline phosphatase, or combinations with ultrasound. Many people may have common bile duct stones in spite of having a negative ultrasound or liver function test. Such people may have to be re-tested with other modalities if the clinical suspicion of common bile duct stones is very high because of their symptoms. False-positive results are also possible and further non-invasive testing is recommended to confirm common bile duct stones to avoid the risks of invasive testing.It should be noted that these results were based on few studies of poor methodological quality and the results for ultrasound varied considerably between studies. Therefore, the results should be interpreted with caution. Further studies of high methodological quality are necessary to determine the diagnostic accuracy of ultrasound and liver function tests.

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.

PubMed

Lu, Zhiyong; Hirschman, Lynette

2012-01-01

Manual curation of data from the biomedical literature is a rate-limiting factor for many expert curated databases. Despite the continuing advances in biomedical text mining and the pressing needs of biocurators for better tools, few existing text-mining tools have been successfully integrated into production literature curation systems such as those used by the expert curated databases. To close this gap and better understand all aspects of literature curation, we invited submissions of written descriptions of curation workflows from expert curated databases for the BioCreative 2012 Workshop Track II. We received seven qualified contributions, primarily from model organism databases. Based on these descriptions, we identified commonalities and differences across the workflows, the common ontologies and controlled vocabularies used and the current and desired uses of text mining for biocuration. Compared to a survey done in 2009, our 2012 results show that many more databases are now using text mining in parts of their curation workflows. In addition, the workshop participants identified text-mining aids for finding gene names and symbols (gene indexing), prioritization of documents for curation (document triage) and ontology concept assignment as those most desired by the biocurators. DATABASE URL: http://www.biocreative.org/tasks/bc-workshop-2012/workflow/.

Realistic simulated MRI and SPECT databases. Application to SPECT/MRI registration evaluation.

PubMed

Aubert-Broche, Berengere; Grova, Christophe; Reilhac, Anthonin; Evans, Alan C; Collins, D Louis

2006-01-01

This paper describes the construction of simulated SPECT and MRI databases that account for realistic anatomical and functional variability. The data is used as a gold-standard to evaluate four SPECT/MRI similarity-based registration methods. Simulation realism was accounted for using accurate physical models of data generation and acquisition. MRI and SPECT simulations were generated from three subjects to take into account inter-subject anatomical variability. Functional SPECT data were computed from six functional models of brain perfusion. Previous models of normal perfusion and ictal perfusion observed in Mesial Temporal Lobe Epilepsy (MTLE) were considered to generate functional variability. We studied the impact noise and intensity non-uniformity in MRI simulations and SPECT scatter correction may have on registration accuracy. We quantified the amount of registration error caused by anatomical and functional variability. Registration involving ictal data was less accurate than registration involving normal data. MR intensity nonuniformity was the main factor decreasing registration accuracy. The proposed simulated database is promising to evaluate many functional neuroimaging methods, involving MRI and SPECT data.

Selection of Suitable Reference Genes for RT-qPCR Normalization under Abiotic Stresses and Hormone Stimulation in Persimmon (Diospyros kaki Thunb)

PubMed Central

Wang, Peihong; Xiong, Aisheng; Gao, Zhihong; Yu, Xinyi; Li, Man; Hou, Yingjun; Sun, Chao; Qu, Shenchun

2016-01-01

The success of quantitative real-time reverse transcription polymerase chain reaction (RT-qPCR) to quantify gene expression depends on the stability of the reference genes used for data normalization. To date, systematic screening for reference genes in persimmon (Diospyros kaki Thunb) has never been reported. In this study, 13 candidate reference genes were cloned from 'Nantongxiaofangshi' using information available in the transcriptome database. Their expression stability was assessed by geNorm and NormFinder algorithms under abiotic stress and hormone stimulation. Our results showed that the most suitable reference genes across all samples were UBC and GAPDH, and not the commonly used persimmon reference gene ACT. In addition, UBC combined with RPII or TUA were found to be appropriate for the "abiotic stress" group and α-TUB combined with PP2A were found to be appropriate for the "hormone stimuli" group. For further validation, the transcript level of the DkDREB2C homologue under heat stress was studied with the selected genes (CYP, GAPDH, TUA, UBC, α-TUB, and EF1-α). The results suggested that it is necessary to choose appropriate reference genes according to the test materials or experimental conditions. Our study will be useful for future studies on gene expression in persimmon. PMID:27513755

Diagnostic and clinical benefit of combined coronary calcium and perfusion assessment in patients undergoing PET/CT myocardial perfusion stress imaging.

PubMed

Bybee, Kevin A; Lee, John; Markiewicz, Richard; Longmore, Ryan; McGhie, A Iain; O'Keefe, James H; Hsu, Bai-Ling; Kennedy, Kevin; Thompson, Randall C; Bateman, Timothy M

2010-04-01

A limitation of stress myocardial perfusion imaging (MPI) is the inability to detect non-obstructive coronary artery disease (CAD). One advantage of MPI with a hybrid CT device is the ability to obtain same-setting measurement of the coronary artery calcium score (CACS). Utilizing our single-center nuclear database, we identified 760 consecutive patients with: (1) no CAD history; (2) a normal clinically indicated Rb-82 PET/CT stress perfusion study; and (3) a same-setting CAC scan. 487 of 760 patients (64.1%) had subclinical CAD based on an abnormal CACS. Of those with CAC, the CACS was > or =100, > or =400, and > or =1000 in 47.0%, 22.4%, and 8.4% of patients, respectively. Less than half of the patients with CAC were receiving aspirin or statin medications prior to PET/CT imaging. Patients with CAC were more likely to be initiated or optimized on proven medical therapy for CAD immediately following PET/CT MPI compared to those without CAC. Subclinical CAD is common in patients without known CAD and normal myocardial perfusion assessed by hybrid PET/CT imaging. Identification of CAC influences subsequent physician prescribing patterns such that those with CAC are more likely to be treated with proven medical therapy for the treatment of CAD.

Bilateral Image Subtraction and Multivariate Models for the Automated Triaging of Screening Mammograms

PubMed Central

Celaya-Padilla, José; Martinez-Torteya, Antonio; Rodriguez-Rojas, Juan; Galvan-Tejada, Jorge; Treviño, Victor; Tamez-Peña, José

2015-01-01

Mammography is the most common and effective breast cancer screening test. However, the rate of positive findings is very low, making the radiologic interpretation monotonous and biased toward errors. This work presents a computer-aided diagnosis (CADx) method aimed to automatically triage mammogram sets. The method coregisters the left and right mammograms, extracts image features, and classifies the subjects into risk of having malignant calcifications (CS), malignant masses (MS), and healthy subject (HS). In this study, 449 subjects (197 CS, 207 MS, and 45 HS) from a public database were used to train and evaluate the CADx. Percentile-rank (p-rank) and z-normalizations were used. For the p-rank, the CS versus HS model achieved a cross-validation accuracy of 0.797 with an area under the receiver operating characteristic curve (AUC) of 0.882; the MS versus HS model obtained an accuracy of 0.772 and an AUC of 0.842. For the z-normalization, the CS versus HS model achieved an accuracy of 0.825 with an AUC of 0.882 and the MS versus HS model obtained an accuracy of 0.698 and an AUC of 0.807. The proposed method has the potential to rank cases with high probability of malignant findings aiding in the prioritization of radiologists work list. PMID:26240818

Experimental and statistical post-validation of positive example EST sequences carrying peroxisome targeting signals type 1 (PTS1)

PubMed Central

Lingner, Thomas; Kataya, Amr R. A.; Reumann, Sigrun

2012-01-01

We recently developed the first algorithms specifically for plants to predict proteins carrying peroxisome targeting signals type 1 (PTS1) from genome sequences.1 As validated experimentally, the prediction methods are able to correctly predict unknown peroxisomal Arabidopsis proteins and to infer novel PTS1 tripeptides. The high prediction performance is primarily determined by the large number and sequence diversity of the underlying positive example sequences, which mainly derived from EST databases. However, a few constructs remained cytosolic in experimental validation studies, indicating sequencing errors in some ESTs. To identify erroneous sequences, we validated subcellular targeting of additional positive example sequences in the present study. Moreover, we analyzed the distribution of prediction scores separately for each orthologous group of PTS1 proteins, which generally resembled normal distributions with group-specific mean values. The cytosolic sequences commonly represented outliers of low prediction scores and were located at the very tail of a fitted normal distribution. Three statistical methods for identifying outliers were compared in terms of sensitivity and specificity.” Their combined application allows elimination of erroneous ESTs from positive example data sets. This new post-validation method will further improve the prediction accuracy of both PTS1 and PTS2 protein prediction models for plants, fungi, and mammals. PMID:22415050

Lung and Heart Sounds Analysis: State-of-the-Art and Future Trends.

PubMed

Padilla-Ortiz, Ana L; Ibarra, David

2018-01-01

Lung sounds, which include all sounds that are produced during the mechanism of respiration, may be classified into normal breath sounds and adventitious sounds. Normal breath sounds occur when no respiratory problems exist, whereas adventitious lung sounds (wheeze, rhonchi, crackle, etc.) are usually associated with certain pulmonary pathologies. Heart and lung sounds that are heard using a stethoscope are the result of mechanical interactions that indicate operation of cardiac and respiratory systems, respectively. In this article, we review the research conducted during the last six years on lung and heart sounds, instrumentation and data sources (sensors and databases), technological advances, and perspectives in processing and data analysis. Our review suggests that chronic obstructive pulmonary disease (COPD) and asthma are the most common respiratory diseases reported on in the literature; related diseases that are less analyzed include chronic bronchitis, idiopathic pulmonary fibrosis, congestive heart failure, and parenchymal pathology. Some new findings regarding the methodologies associated with advances in the electronic stethoscope have been presented for the auscultatory heart sound signaling process, including analysis and clarification of resulting sounds to create a diagnosis based on a quantifiable medical assessment. The availability of automatic interpretation of high precision of heart and lung sounds opens interesting possibilities for cardiovascular diagnosis as well as potential for intelligent diagnosis of heart and lung diseases.

Experimental and statistical post-validation of positive example EST sequences carrying peroxisome targeting signals type 1 (PTS1).

PubMed

Lingner, Thomas; Kataya, Amr R A; Reumann, Sigrun

2012-02-01

We recently developed the first algorithms specifically for plants to predict proteins carrying peroxisome targeting signals type 1 (PTS1) from genome sequences. As validated experimentally, the prediction methods are able to correctly predict unknown peroxisomal Arabidopsis proteins and to infer novel PTS1 tripeptides. The high prediction performance is primarily determined by the large number and sequence diversity of the underlying positive example sequences, which mainly derived from EST databases. However, a few constructs remained cytosolic in experimental validation studies, indicating sequencing errors in some ESTs. To identify erroneous sequences, we validated subcellular targeting of additional positive example sequences in the present study. Moreover, we analyzed the distribution of prediction scores separately for each orthologous group of PTS1 proteins, which generally resembled normal distributions with group-specific mean values. The cytosolic sequences commonly represented outliers of low prediction scores and were located at the very tail of a fitted normal distribution. Three statistical methods for identifying outliers were compared in terms of sensitivity and specificity." Their combined application allows elimination of erroneous ESTs from positive example data sets. This new post-validation method will further improve the prediction accuracy of both PTS1 and PTS2 protein prediction models for plants, fungi, and mammals.

Nonproliferative and Proliferative Lesions of the Rat and Mouse Female Reproductive System

PubMed Central

Dixon, Darlene; Alison, Roger; Bach, Ute; Colman, Karyn; Foley, George L.; Harleman, Johannes H.; Haworth, Richard; Herbert, Ronald; Heuser, Anke; Long, Gerald; Mirsky, Michael; Regan, Karen; Van Esch, Eric; Westwood, F. Russell; Vidal, Justin; Yoshida, Midori

2014-01-01

The INHAND (International Harmonization of Nomenclature and Diagnostic Criteria for Lesions in Rats and Mice) Project (www.toxpath.org/inhand.asp) is a joint initiative of the Societies of Toxicological Pathology from Europe (ESTP), Great Britain (BSTP), Japan (JSTP) and North America (STP) to develop an internationally accepted nomenclature for proliferative and nonproliferative lesions in laboratory animals. The purpose of this publication is to provide a standardized nomenclature for classifying microscopic lesions observed in the female reproductive tract of laboratory rats and mice, with color photomicrographs illustrating examples of some lesions. The standardized nomenclature presented in this document is also available electronically on the internet (http://www.goreni.org/). Sources of material included histopathology databases from government, academia, and industrial laboratories throughout the world. Content includes spontaneous and aging lesions as well as lesions induced by exposure to test materials. There is also a section on normal cyclical changes observed in the ovary, uterus, cervix and vagina to compare normal physiological changes with pathological lesions. A widely accepted and utilized international harmonization of nomenclature for female reproductive tract lesions in laboratory animals will decrease confusion among regulatory and scientific research organizations in different countries and provide a common language to increase and enrich international exchanges of information among toxicologists and pathologists. PMID:25516636

LocExpress: a web server for efficiently estimating expression of novel transcripts.

PubMed

Hou, Mei; Tian, Feng; Jiang, Shuai; Kong, Lei; Yang, Dechang; Gao, Ge

2016-12-22

The temporal and spatial-specific expression pattern of a transcript in multiple tissues and cell types can indicate key clues about its function. While several gene atlas available online as pre-computed databases for known gene models, it's still challenging to get expression profile for previously uncharacterized (i.e. novel) transcripts efficiently. Here we developed LocExpress, a web server for efficiently estimating expression of novel transcripts across multiple tissues and cell types in human (20 normal tissues/cells types and 14 cell lines) as well as in mouse (24 normal tissues/cell types and nine cell lines). As a wrapper to RNA-Seq quantification algorithm, LocExpress efficiently reduces the time cost by making abundance estimation calls increasingly within the minimum spanning bundle region of input transcripts. For a given novel gene model, such local context-oriented strategy allows LocExpress to estimate its FPKMs in hundreds of samples within minutes on a standard Linux box, making an online web server possible. To the best of our knowledge, LocExpress is the only web server to provide nearly real-time expression estimation for novel transcripts in common tissues and cell types. The server is publicly available at http://loc-express.cbi.pku.edu.cn .

YAdumper: extracting and translating large information volumes from relational databases to structured flat files.

PubMed

Fernández, José M; Valencia, Alfonso

2004-10-12

Downloading the information stored in relational databases into XML and other flat formats is a common task in bioinformatics. This periodical dumping of information requires considerable CPU time, disk and memory resources. YAdumper has been developed as a purpose-specific tool to deal with the integral structured information download of relational databases. YAdumper is a Java application that organizes database extraction following an XML template based on an external Document Type Declaration. Compared with other non-native alternatives, YAdumper substantially reduces memory requirements and considerably improves writing performance.

Universal Index System

NASA Technical Reports Server (NTRS)

Kelley, Steve; Roussopoulos, Nick; Sellis, Timos; Wallace, Sarah

1993-01-01

The Universal Index System (UIS) is an index management system that uses a uniform interface to solve the heterogeneity problem among database management systems. UIS provides an easy-to-use common interface to access all underlying data, but also allows different underlying database management systems, storage representations, and access methods.

National Nutrient Database for Standard Reference - Find Nutrient Value of Common Foods by Nutrient

MedlinePlus

... grams Household * required field ​ USDA Food Composition Databases Software developed by the National Agricultural Library v.3.9.4.1 2018-06-11 NAL Home | USDA.gov | Agricultural Research Service | Plain Language | FOIA | Accessibility Statement | Information Quality | Privacy ...

Integrating magnetic resonance imaging postprocessing results into neuronavigation for electrode implantation and resection of subtle focal cortical dysplasia in previously cryptogenic epilepsy.

PubMed

Wellmer, Jörg; Parpaley, Yaroslav; von Lehe, Marec; Huppertz, Hans-Jürgen

2010-01-01

Focal cortical dysplasias (FCDs) are highly epileptogenic lesions. Surgical removal is frequently the best treatment option for pharmacoresistant epilepsy. However, subtle FCDs may remain undetected even after high-resolution magnetic resonance imaging (MRI). Morphometric MRI analysis, which compares the individual brain with a normal database, can facilitate the detection of FCDs. We describe how the results of normal database-based MRI postprocessing can be used to guide stereotactic electrode implantation and subsequent resection of lesions that are suspected to be FCDs. A presurgical evaluation was conducted on a 19-year-old woman with pharmacoresistant hypermotor seizures. Conventional high-resolution MRI was classified as negative for epileptogenic lesions. However, morphometric analysis of the spatially normalized MRI revealed abnormal gyration and blurring of the gray-white matter junction, which was suggestive of a small and deeply seated FCD in the left frontal lobe. The brain region highlighted by morphometric analysis was marked as a region of interest, transferred back to the original dimension of the individual MRI, and imported into a neuronavigation system. This allowed the region of interest-targeted stereotactic implantation of 2 depth electrodes, by which seizure onset was confirmed in the lesion. The electrodes also guided the final resection, which rendered the patient seizure-free. The lesion was histologically classified as FCD Palmini and Lüders IIB. Transferring normal database-based MRI postprocessing results into a neuronavigation system is a new and worthwhile extension of multimodal neuronavigation. The combination of resulting regions of interest with functional and anatomic data may facilitate planning of electrode implantation for invasive electroencephalographic recordings and the final resection of small or deeply seated FCDs.

Extracting patterns of database and software usage from the bioinformatics literature

PubMed Central

Duck, Geraint; Nenadic, Goran; Brass, Andy; Robertson, David L.; Stevens, Robert

2014-01-01

Motivation: As a natural consequence of being a computer-based discipline, bioinformatics has a strong focus on database and software development, but the volume and variety of resources are growing at unprecedented rates. An audit of database and software usage patterns could help provide an overview of developments in bioinformatics and community common practice, and comparing the links between resources through time could demonstrate both the persistence of existing software and the emergence of new tools. Results: We study the connections between bioinformatics resources and construct networks of database and software usage patterns, based on resource co-occurrence, that correspond to snapshots of common practice in the bioinformatics community. We apply our approach to pairings of phylogenetics software reported in the literature and argue that these could provide a stepping stone into the identification of scientific best practice. Availability and implementation: The extracted resource data, the scripts used for network generation and the resulting networks are available at http://bionerds.sourceforge.net/networks/ Contact: robert.stevens@manchester.ac.uk PMID:25161253

Mining databases for protein aggregation: a review.

PubMed

Tsiolaki, Paraskevi L; Nastou, Katerina C; Hamodrakas, Stavros J; Iconomidou, Vassiliki A

2017-09-01

Protein aggregation is an active area of research in recent decades, since it is the most common and troubling indication of protein instability. Understanding the mechanisms governing protein aggregation and amyloidogenesis is a key component to the aetiology and pathogenesis of many devastating disorders, including Alzheimer's disease or type 2 diabetes. Protein aggregation data are currently found "scattered" in an increasing number of repositories, since advances in computational biology greatly influence this field of research. This review exploits the various resources of aggregation data and attempts to distinguish and analyze the biological knowledge they contain, by introducing protein-based, fragment-based and disease-based repositories, related to aggregation. In order to gain a broad overview of the available repositories, a novel comprehensive network maps and visualizes the current association between aggregation databases and other important databases and/or tools and discusses the beneficial role of community annotation. The need for unification of aggregation databases in a common platform is also addressed.

BioMart Central Portal: an open database network for the biological community.

PubMed

Guberman, Jonathan M; Ai, J; Arnaiz, O; Baran, Joachim; Blake, Andrew; Baldock, Richard; Chelala, Claude; Croft, David; Cros, Anthony; Cutts, Rosalind J; Di Génova, A; Forbes, Simon; Fujisawa, T; Gadaleta, E; Goodstein, D M; Gundem, Gunes; Haggarty, Bernard; Haider, Syed; Hall, Matthew; Harris, Todd; Haw, Robin; Hu, S; Hubbard, Simon; Hsu, Jack; Iyer, Vivek; Jones, Philip; Katayama, Toshiaki; Kinsella, R; Kong, Lei; Lawson, Daniel; Liang, Yong; Lopez-Bigas, Nuria; Luo, J; Lush, Michael; Mason, Jeremy; Moreews, Francois; Ndegwa, Nelson; Oakley, Darren; Perez-Llamas, Christian; Primig, Michael; Rivkin, Elena; Rosanoff, S; Shepherd, Rebecca; Simon, Reinhard; Skarnes, B; Smedley, Damian; Sperling, Linda; Spooner, William; Stevenson, Peter; Stone, Kevin; Teague, J; Wang, Jun; Wang, Jianxin; Whitty, Brett; Wong, D T; Wong-Erasmus, Marie; Yao, L; Youens-Clark, Ken; Yung, Christina; Zhang, Junjun; Kasprzyk, Arek

2011-01-01

BioMart Central Portal is a first of its kind, community-driven effort to provide unified access to dozens of biological databases spanning genomics, proteomics, model organisms, cancer data, ontology information and more. Anybody can contribute an independently maintained resource to the Central Portal, allowing it to be exposed to and shared with the research community, and linking it with the other resources in the portal. Users can take advantage of the common interface to quickly utilize different sources without learning a new system for each. The system also simplifies cross-database searches that might otherwise require several complicated steps. Several integrated tools streamline common tasks, such as converting between ID formats and retrieving sequences. The combination of a wide variety of databases, an easy-to-use interface, robust programmatic access and the array of tools make Central Portal a one-stop shop for biological data querying. Here, we describe the structure of Central Portal and show example queries to demonstrate its capabilities.

A Scandinavian experience of register collaboration: the Nordic Arthroplasty Register Association (NARA).

PubMed

Havelin, Leif I; Robertsson, Otto; Fenstad, Anne M; Overgaard, Søren; Garellick, Göran; Furnes, Ove

2011-12-21

The Nordic (Scandinavian) countries have had working arthroplasty registers for several years. However, the small numbers of inhabitants and the conformity within each country with respect to preferred prosthesis brands and techniques have limited register research. A collaboration called NARA (Nordic Arthroplasty Register Association) was started in 2007, resulting in a common database for Denmark, Norway, and Sweden with regard to hip replacements in 2008 and primary knee replacements in 2009. Finland joined the project in 2010. A code set was defined for the parameters that all registers had in common, and data were re-coded, within each national register, according to the common definitions. After de-identification of the patients, the anonymous data were merged into a common database. The first study based on this common database included 280,201 hip arthroplasties and the second, 151,814 knee arthroplasties. Kaplan-Meier and Cox multiple regression analyses, with adjustment for age, sex, and diagnosis, were used to calculate prosthesis survival, with any revision as the end point. In later studies, specific reasons for revision were also used as end points. We found differences among the countries concerning patient demographics, preferred surgical approaches, fixation methods, and prosthesis brands. Prosthesis survival was best in Sweden, where cement implant fixation was used more commonly than it was in the other countries. As the comparison of national results was one of the main initial aims of this collaboration, only parameters and data that all three registers could deliver were included in the database. Compared with each separate register, this combined register resulted in reduced numbers of parameters and details. In future collaborations of registers with a focus on comparing the performances of prostheses and articulations, we should probably include only the data needed specifically for the predetermined purposes, from registers that can deliver these data, rather than compiling all data from all registers that are willing to participate.

Update of the androgen receptor gene mutations database.

PubMed

Gottlieb, B; Beitel, L K; Lumbroso, R; Pinsky, L; Trifiro, M

1999-01-01

The current version of the androgen receptor (AR) gene mutations database is described. The total number of reported mutations has risen from 309 to 374 during the past year. We have expanded the database by adding information on AR-interacting proteins; and we have improved the database by identifying those mutation entries that have been updated. Mutations of unknown significance have now been reported in both the 5' and 3' untranslated regions of the AR gene, and in individuals who are somatic mosaics constitutionally. In addition, single nucleotide polymorphisms, including silent mutations, have been discovered in normal individuals and in individuals with male infertility. A mutation hotspot associated with prostatic cancer has been identified in exon 5. The database is available on the internet (http://www.mcgill.ca/androgendb/), from EMBL-European Bioinformatics Institute (ftp.ebi.ac.uk/pub/databases/androgen), or as a Macintosh FilemakerPro or Word file (MC33@musica.mcgill.ca). Copyright 1999 Wiley-Liss, Inc.

Reactive gastropathy is associated with inflammatory conditions throughout the gastrointestinal tract.

PubMed

Maguilnik, I; Neumann, W L; Sonnenberg, A; Genta, R M

2012-10-01

The epidemiology of reactive gastropathy and its relationship with other conditions of the gastrointestinal tract associated with NSAID use have not been evaluated. To test the hypothesis that if reactive gastropathy shares common aetiological factors with these conditions, the analysis of a large cohort would unveil associations. We queried a national pathology database for subjects with a diagnosis of reactive gastropathy; controls were patients with normal gastric biopsies. We also extracted diagnoses of H. pylori infection, intestinal metaplasia, duodenal lymphocytosis, duodenitis, ileitis, microscopic colitis and focal colitis. Of 504 011 patients with gastric biopsies, 69 101 had oesophageal, 166 134 duodenal, 13 010 ileal and 83 334 colonic biopsies. Reactive gastropathy was diagnosed in 15.6% of patients, H. pylori infection in 10.3% and normal gastric mucosa in 16.3%. Reactive gastropathy was evenly distributed across the US and increased from 2.0% in the first decade of life to >20% in octogenarians. Compared with controls, reactive gastropathy was significantly associated with Barrett's mucosa (OR 1.21 95% CI 1.16-129); duodenitis (OR 1.36; 95% CI 1.28-1.44); duodenal intraepithelial lymphocytosis (OR 1.25; 95% CI 1.13-1.39); active ileitis (OR 1.88; 95% CI 1.47-2.40); focal active colitis (OR 1.57; 95% CI 1.33-1.86); and collagenous colitis (OR 1.50; 95% CI 1.12-2.03). Reactive gastropathy, a common histopathological feature of the stomach, shows an age-dependent rise and is associated with changes of the digestive tract believed to be caused by NSAID use or duodenogastric reflux. However, a large fraction of reactive gastropathy remains unexplained; its frequent occurrence merits further efforts at elucidating its aetiology. © 2012 Blackwell Publishing Ltd.

Is there consensus in defining childhood cerebral visual impairment? A systematic review of terminology and definitions.

PubMed

Sakki, Hanna E A; Dale, Naomi J; Sargent, Jenefer; Perez-Roche, Teresa; Bowman, Richard

2018-04-01

The childhood condition of visual difficulties caused by brain damage, commonly termed cortical or cerebral visual impairment (CVI), is well established but has no internationally accepted definition. Clarification of its core features is required to advance research and clinical practice. This systematic review aimed to identify the definitions of childhood CVI in the original scientific literature to describe and critically appraise a consensual definition of the condition. MEDLINE, EMBASE, PsychINFO, CINAHL and AMED databases were searched in January 2017. Studies were included if they (1) were published original research, (2) contained a childhood CVI sample, (3) contained a definition of CVI and (4) described their CVI identification/diagnostic method. Thematic analysis identified concepts within definitions and narrative synthesis was conducted. Of 1150 articles, 51 met inclusion criteria. Definitions were subdivided according to detail (descriptive definition, description not reaching definition status and diagnostic/operationalising criteria). Three themes concerning visual deficits, eye health and brain integrity were identified (each containing subthemes) and analysed individually across definitions. The most common themes were ' visual impairment' (n=20), 'retrochiasmatic pathway damage'(n=13) and 'normal/near normal eye health' (n=15). The most consensual definition identified here may not be the best quality for advancing our understanding of CVI. We argue for the alternative definition: CVI is a verifiable visual dysfunction which cannot be attributed to disorders of the anterior visual pathways or any potentially co-occurring ocular impairment. We propose reporting guidelines to permit comparison across studies and increase the evidence base for more reliable clinical assessment and diagnosis. © 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.

Gene-expression analysis of cold-stress response in the sexually transmitted protist Trichomonas vaginalis.

PubMed

Fang, Yi-Kai; Huang, Kuo-Yang; Huang, Po-Jung; Lin, Rose; Chao, Mei; Tang, Petrus

2015-12-01

Trichomonas vaginalis is the etiologic agent of trichomoniasis, the most common nonviral sexually transmitted disease in the world. This infection affects millions of individuals worldwide annually. Although direct sexual contact is the most common mode of transmission, increasing evidence indicates that T. vaginalis can survive in the external environment and can be transmitted by contaminated utensils. We found that the growth of T. vaginalis under cold conditions is greatly inhibited, but recovers after placing these stressed cells at the normal cultivation temperature of 37 °C. However, the mechanisms by which T. vaginalis regulates this adaptive process are unclear. An expressed sequence tag (EST) database generated from a complementary DNA library of T. vaginalis messenger RNAs expressed under cold-culture conditions (4 °C, TvC) was compared with a previously published normal-cultured EST library (37 °C, TvE) to assess the cold-stress responses of T. vaginalis. A total of 9780 clones were sequenced from the TvC library and were mapped to 2934 genes in the T. vaginalis genome. A total of 1254 genes were expressed in both the TvE and TvC libraries, and 1680 genes were only found in the TvC library. A functional analysis showed that cold temperature has effects on many cellular mechanisms, including increased H2O2 tolerance, activation of the ubiquitin-proteasome system, induction of iron-sulfur cluster assembly, and reduced energy metabolism and enzyme expression. The current study is the first large-scale transcriptomic analysis in cold-stressed T. vaginalis and the results enhance our understanding of this important protist. Copyright © 2014. Published by Elsevier B.V.

Normalizing suffering: A meta-synthesis of experiences of and perspectives on pain and pain management in nursing homes

PubMed Central

Vaismoradi, Mojtaba; Skär, Lisa; Söderberg, Siv; Bondas, Terese E.

2016-01-01

Older people who live in nursing homes commonly suffer from pain. Therefore, relieving suffering among older people that stems from pain demands knowledge improvement through an integration of international knowledge. This study aimed to integrate current international findings and strengthen the understanding of older people's experiences of and perspectives on pain and pain management in nursing homes. A meta-synthesis study using Noblit and Hare's interpretative meta-ethnography approach was conducted. Empirical research papers from journals were collected from various databases. The search process and appraisal determined six articles for inclusion. Two studies were conducted in the US and one each in Iceland, Norway, the UK, and Australia. The older people's experiences of pain as well as perspectives on pain management from all involved (older people, their family members, and healthcare staff) were integrated into a theoretical model using three themes of “identity of pain,” “recognition of pain,” and “response to pain.” The metaphor of “normalizing suffering” was devised to illustrate the meaning of pain experiences and pain management in nursing homes. Society's common attitude that pain is unavoidable and therefore acceptable in old age in society—among older people themselves as well as those who are responsible for reporting, acknowledging, and relieving pain—must change. The article emphasizes that pain as a primary source of suffering can be relieved, provided that older people are encouraged to report their pain. In addition, healthcare staff require sufficient training to take a person-centered approach towards assessment and management of pain that considers all elements of pain. PMID:27173102

New extension software modules to enhance searching and display of transcriptome data in Tripal databases

PubMed Central

Chen, Ming; Henry, Nathan; Almsaeed, Abdullah; Zhou, Xiao; Wegrzyn, Jill; Ficklin, Stephen

2017-01-01

Abstract Tripal is an open source software package for developing biological databases with a focus on genetic and genomic data. It consists of a set of core modules that deliver essential functions for loading and displaying data records and associated attributes including organisms, sequence features and genetic markers. Beyond the core modules, community members are encouraged to contribute extension modules to build on the Tripal core and to customize Tripal for individual community needs. To expand the utility of the Tripal software system, particularly for RNASeq data, we developed two new extension modules. Tripal Elasticsearch enables fast, scalable searching of the entire content of a Tripal site as well as the construction of customized advanced searches of specific data types. We demonstrate the use of this module for searching assembled transcripts by functional annotation. A second module, Tripal Analysis Expression, houses and displays records from gene expression assays such as RNA sequencing. This includes biological source materials (biomaterials), gene expression values and protocols used to generate the data. In the case of an RNASeq experiment, this would reflect the individual organisms and tissues used to produce sequencing libraries, the normalized gene expression values derived from the RNASeq data analysis and a description of the software or code used to generate the expression values. The module will load data from common flat file formats including standard NCBI Biosample XML. Data loading, display options and other configurations can be controlled by authorized users in the Drupal administrative backend. Both modules are open source, include usage documentation, and can be found in the Tripal organization’s GitHub repository. Database URL: Tripal Elasticsearch module: https://github.com/tripal/tripal_elasticsearch Tripal Analysis Expression module: https://github.com/tripal/tripal_analysis_expression PMID:29220446

A storage scheme for the real-time database supporting the on-line commitment

NASA Astrophysics Data System (ADS)

Dai, Hong-bin; Jing, Yu-jian; Wang, Hui

2013-07-01

The modern SCADA (Supervisory Control and Data acquisition) systems have been applied to various aspects of everyday life. As the time goes on, the requirements of the applications of the systems vary. Thus the data structure of the real-time database, which is the core of a SCADA system, often needs modification. As a result, the commitment consisting of a sequence of configuration operations modifying the data structure of the real-time database is performed from time to time. Though it is simple to perform the off-line commitment by first stopping and then restarting the system, during which all the data in the real-time database are reconstructed. It is much more preferred or in some cases even necessary to perform the on-line commitment, during which the real-time database can still provide real-time service and the system continues working normally. In this paper, a storage scheme of the data in the real-time database is proposed. It helps the real-time database support its on-line commitment, during which real-time service is still available.

Evaluation and validity of a LORETA normative EEG database.

PubMed

Thatcher, R W; North, D; Biver, C

2005-04-01

To evaluate the reliability and validity of a Z-score normative EEG database for Low Resolution Electromagnetic Tomography (LORETA), EEG digital samples (2 second intervals sampled 128 Hz, 1 to 2 minutes eyes closed) were acquired from 106 normal subjects, and the cross-spectrum was computed and multiplied by the Key Institute's LORETA 2,394 gray matter pixel T Matrix. After a log10 transform or a Box-Cox transform the mean and standard deviation of the *.lor files were computed for each of the 2394 gray matter pixels, from 1 to 30 Hz, for each of the subjects. Tests of Gaussianity were computed in order to best approximate a normal distribution for each frequency and gray matter pixel. The relative sensitivity of a Z-score database was computed by measuring the approximation to a Gaussian distribution. The validity of the LORETA normative database was evaluated by the degree to which confirmed brain pathologies were localized using the LORETA normative database. Log10 and Box-Cox transforms approximated Gaussian distribution in the range of 95.64% to 99.75% accuracy. The percentage of normative Z-score values at 2 standard deviations ranged from 1.21% to 3.54%, and the percentage of Z-scores at 3 standard deviations ranged from 0% to 0.83%. Left temporal lobe epilepsy, right sensory motor hematoma and a right hemisphere stroke exhibited maximum Z-score deviations in the same locations as the pathologies. We conclude: (1) Adequate approximation to a Gaussian distribution can be achieved using LORETA by using a log10 transform or a Box-Cox transform and parametric statistics, (2) a Z-Score normative database is valid with adequate sensitivity when using LORETA, and (3) the Z-score LORETA normative database also consistently localized known pathologies to the expected Brodmann areas as an hypothesis test based on the surface EEG before computing LORETA.

The Porcelain Crab Transcriptome and PCAD, the Porcelain Crab Microarray and Sequence Database

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

Tagmount, Abderrahmane; Wang, Mei; Lindquist, Erika

2010-01-27

Background: With the emergence of a completed genome sequence of the freshwater crustacean Daphnia pulex, construction of genomic-scale sequence databases for additional crustacean sequences are important for comparative genomics and annotation. Porcelain crabs, genus Petrolisthes, have been powerful crustacean models for environmental and evolutionary physiology with respect to thermal adaptation and understanding responses of marine organisms to climate change. Here, we present a large-scale EST sequencing and cDNA microarray database project for the porcelain crab Petrolisthes cinctipes. Methodology/Principal Findings: A set of ~;;30K unique sequences (UniSeqs) representing ~;;19K clusters were generated from ~;;98K high quality ESTs from a set ofmore » tissue specific non-normalized and mixed-tissue normalized cDNA libraries from the porcelain crab Petrolisthes cinctipes. Homology for each UniSeq was assessed using BLAST, InterProScan, GO and KEGG database searches. Approximately 66percent of the UniSeqs had homology in at least one of the databases. All EST and UniSeq sequences along with annotation results and coordinated cDNA microarray datasets have been made publicly accessible at the Porcelain Crab Array Database (PCAD), a feature-enriched version of the Stanford and Longhorn Array Databases.Conclusions/Significance: The EST project presented here represents the third largest sequencing effort for any crustacean, and the largest effort for any crab species. Our assembly and clustering results suggest that our porcelain crab EST data set is equally diverse to the much larger EST set generated in the Daphnia pulex genome sequencing project, and thus will be an important resource to the Daphnia research community. Our homology results support the pancrustacea hypothesis and suggest that Malacostraca may be ancestral to Branchiopoda and Hexapoda. Our results also suggest that our cDNA microarrays cover as much of the transcriptome as can reasonably be captured in EST library sequencing approaches, and thus represent a rich resource for studies of environmental genomics.« less

OSTA commonality analysis, volume 2

NASA Technical Reports Server (NTRS)

Stolarik, E. G.

1981-01-01

The 13 OSTA disciplines are examined and the applications being performed under each discipline and the parameter requirements associated with the various applications are identified. It contains a variety of printouts from the commonality database built using DRS on the Vax. It also shows commonality of parameter requirements by discipline and by application.

Choosing the Right Database Management Program.

ERIC Educational Resources Information Center

Vockell, Edward L.; Kopenec, Donald

1989-01-01

Provides a comparison of four database management programs commonly used in schools: AppleWorks, the DOS 3.3 and ProDOS versions of PFS, and MECC's Data Handler. Topics discussed include information storage, spelling checkers, editing functions, search strategies, graphs, printout formats, library applications, and HyperCard. (LRW)

Quality control of EUVE databases

NASA Technical Reports Server (NTRS)

John, L. M.; Drake, J.

1992-01-01

The publicly accessible databases for the Extreme Ultraviolet Explorer include: the EUVE Archive mailserver; the CEA ftp site; the EUVE Guest Observer Mailserver; and the Astronomical Data System node. The EUVE Performance Assurance team is responsible for verifying that these public EUVE databases are working properly, and that the public availability of EUVE data contained therein does not infringe any data rights which may have been assigned. In this poster, we describe the Quality Assurance (QA) procedures we have developed from the approach of QA as a service organization, thus reflecting the overall EUVE philosophy of Quality Assurance integrated into normal operating procedures, rather than imposed as an external, post facto, control mechanism.

EarthRef.org: Exploring aspects of a Cyber Infrastructure in Earth Science and Education

NASA Astrophysics Data System (ADS)

Staudigel, H.; Koppers, A.; Tauxe, L.; Constable, C.; Helly, J.

2004-12-01

EarthRef.org is the common host and (co-) developer of a range of earth science databases and IT resources providing a test bed for a Cyberinfrastructure in Earth Science and Education (CIESE). EarthRef.org data base efforts include in particular the Geochemical Earth Reference Model (GERM), the Magnetics Information Consortium (MagIC), the Educational Resources for Earth Science Education (ERESE) project, the Seamount Catalog, the Mid-Ocean Ridge Catalog, the Radio-Isotope Geochronology (RiG) initiative for CHRONOS, and the Microbial Observatory for Fe oxidizing microbes on Loihi Seamount (FeMO; the most recent development). These diverse databases are developed under a single database umbrella and webserver at the San Diego Supercomputing Center. All the data bases have similar structures, with consistent metadata concepts, a common database layout, and automated upload wizards. Shared resources include supporting databases like an address book, a reference/publication catalog, and a common digital archive making database development and maintenance cost-effective, while guaranteeing interoperability. The EarthRef.org CIESE provides a common umbrella for synthesis information as well as sample-based data, and it bridges the gap between science and science education in middle and high schools, validating the potential for a system wide data infrastructure in a CIESE. EarthRef.org experiences have shown that effective communication with the respective communities is a key part of a successful CIESE facilitating both utility and community buy-in. GERM has been particularly successful at developing a metadata scheme for geochemistry and in the development of a new electronic journal (G-cubed) that has made much progress in data publication and linkages between journals and community data bases. GERM also has worked, through editors and publishers, towards interfacing databases with the publication process, to accomplish a more scholarly and database friendly data publication environment, and to interface with the respective science communities. MagIC has held several workshops that have resulted in an integrated data archival environment using metadata that are interchangeable with the geochemical metadata. MagIC archives a wide array of paleo and rock magnetic directional, intensity and magnetic property data as well as integrating computational tools. ERESE brought together librarians, teachers, and scientists to create an educational environment that supports inquiry driven education and the use of science data. Experiences in EarthRef.org demonstrates the feasibility of an effective, community wide CIESE for data publication, archival and modeling, as well as the outreach to the educational community.

Prevalence of acid-reducing agents (ARA) in cancer populations and ARA drug-drug interaction potential for molecular targeted agents in clinical development.

PubMed

Smelick, Gillian S; Heffron, Timothy P; Chu, Laura; Dean, Brian; West, David A; Duvall, Scott L; Lum, Bert L; Budha, Nageshwar; Holden, Scott N; Benet, Leslie Z; Frymoyer, Adam; Dresser, Mark J; Ware, Joseph A

2013-11-04

Acid-reducing agents (ARAs) are the most commonly prescribed medications in North America and Western Europe. There are currently no data describing the prevalence of their use among cancer patients. However, this is a paramount question due to the potential for significant drug-drug interactions (DDIs) between ARAs, most commonly proton pump inhibitors (PPIs), and orally administered cancer therapeutics that display pH-dependent solubility, which may lead to decreased drug absorption and decreased therapeutic benefit. Of recently approved orally administered cancer therapeutics, >50% are characterized as having pH-dependent solubility, but there are currently no data describing the potential for this ARA-DDI liability among targeted agents currently in clinical development. The objectives of this study were to (1) determine the prevalence of ARA use among different cancer populations and (2) investigate the prevalence of orally administered cancer therapeutics currently in development that may be liable for an ARA-DDI. To address the question of ARA use among cancer patients, a retrospective cross-sectional analysis was performed using two large healthcare databases: Thomson Reuters MarketScan (N = 1,776,443) and the U.S. Department of Veterans Affairs (VA, N = 1,171,833). Among all cancer patients, the total prevalence proportion of ARA use (no. of cancer patients receiving an ARA/total no. of cancer patients) was 20% and 33% for the MarketScan and VA databases, respectively. PPIs were the most commonly prescribed agent, comprising 79% and 65% of all cancer patients receiving a prescription for an ARA (no. of cancer patients receiving a PPI /no. of cancer patients receiving an ARA) for the MarketScan and VA databases, respectively. To estimate the ARA-DDI liability of orally administered molecular targeted cancer therapeutics currently in development, two publicly available databases, (1) Kinase SARfari and (2) canSAR, were examined. For those orally administered clinical candidates that had available structures, the pKa's and corresponding relative solubilities were calculated for a normal fasting pH of 1.2 and an "ARA-hypochlorhydric" pH of 4. Taking calculated pKa's and relative solubilities into consideration, clinical candidates were classified based on their risk for an ARA-DDI. More than one-quarter (28%) of the molecules investigated are at high risk for an ARA-DDI, and of those high risk molecules, nearly three-quarters (73%) are being clinically evaluated for at least one of five cancer types with the highest prevalence of ARA use (gastrointestinal, pancreatic, lung, glioblastoma multiforme, gastrointestinal stromal tumor (GIST)). These data strongly suggest that with the clinical development of ARA-DDI-susceptible cancer therapeutics will come continued challenges for drug-development scientists, oncologists, and regulatory agencies in ensuring that patients achieve safe and efficacious exposures of their cancer therapeutics and thus optimal patient outcomes.

Geochemical databases: minding the pitfalls to avoid the pratfalls

NASA Astrophysics Data System (ADS)

Goldstein, S. L.; Hofmann, A. W.

2011-12-01

The field of geochemistry has been revolutionized in recent years by the advent of databases (PetDB, GEOROC, NAVDAT, etc). A decade ago, a geochemical synthesis required major time investments in order to compile relatively small amounts of fragmented data from large numbers of publications, Now virtually all of the published data on nearly any solid Earth topic can be downloaded to nearly any desktop computer with a few mouse clicks. Most solid Earth talks at international meetings show data compilations from these databases. Applications of the data are playing an increasingly important role in shaping our thinking about the Earth. They have changed some fundamental ideas about the compositional structure of the Earth (for example, showing that the Earth's "trace element depleted upper mantle" is not so depleted in trace elements). This abundance of riches also poses new risks. Until recently, important details associated with data publication (adequate metadata and quality control information) were given low priority, even in major journals. The online databases preserve whatever has been published, irrespective of quality. "Bad data" arises from many causes, here are a few. Some are associated with sample processing, including incomplete dissolution of refractory trace minerals, or inhomogeneous powders, or contamination of key elements during preparation (for example, this was a problem for lead when gasoline was leaded, and for niobium when tungsten-carbide mills were used to powder samples). Poor analytical quality is a continual problem (for example, when elemental abundances are at near background levels for an analytical method). Errors in published data tables (more common than you think) become bad data in the databases. The accepted values of interlaboratory standards change with time, while the published data based on old values stay the same. Thus the pitfalls associated with the new data accessibility are dangerous in the hands of the inexperienced users (for example, a student of mine took the initiative to write a paper showing very creative insights, based on some neodymium isotope data on oceanic volcanics; unfortunately the uniqueness of the data reflected the normalization procedures used by different labs). Many syntheses assume random sampling even though we know that oversampled regions are over-represented. We will show examples where raw downloads of data from databases without extensive screening can yield data collections where the garbage swamps the useful information. We will also show impressive but meaningless correlations (e.g. upper-mantle temperature versus atmospheric temperature). In order to avoid the pratfalls, screening of database output is necessary. In order to generate better data consistency, new standards for reporting geochemical data are necessary.

Structural Inventory of Great Basin Geothermal Systems and Definition of Favorable Structural Settings

DOE Data Explorer

Faulds, James E.

2013-12-31

Over the course of the entire project, field visits were made to 117 geothermal systems in the Great Basin region. Major field excursions, incorporating visits to large groups of systems, were conducted in western Nevada, central Nevada, northwestern Nevada, northeastern Nevada, east‐central Nevada, eastern California, southern Oregon, and western Utah. For example, field excursions to the following areas included visits of multiple geothermal systems: - Northwestern Nevada: Baltazor Hot Spring, Blue Mountain, Bog Hot Spring, Dyke Hot Springs, Howard Hot Spring, MacFarlane Hot Spring, McGee Mountain, and Pinto Hot Springs in northwest Nevada. - North‐central to northeastern Nevada: Beowawe, Crescent Valley (Hot Springs Point), Dann Ranch (Hand‐me‐Down Hot Springs), Golconda, and Pumpernickel Valley (Tipton Hot Springs) in north‐central to northeast Nevada. - Eastern Nevada: Ash Springs, Chimney Hot Spring, Duckwater, Hiko Hot Spring, Hot Creek Butte, Iverson Spring, Moon River Hot Spring, Moorman Spring, Railroad Valley, and Williams Hot Spring in eastern Nevada. - Southwestern Nevada‐eastern California: Walley’s Hot Spring, Antelope Valley, Fales Hot Springs, Buckeye Hot Springs, Travertine Hot Springs, Teels Marsh, Rhodes Marsh, Columbus Marsh, Alum‐Silver Peak, Fish Lake Valley, Gabbs Valley, Wild Rose, Rawhide‐ Wedell Hot Springs, Alkali Hot Springs, and Baileys/Hicks/Burrell Hot Springs. - Southern Oregon: Alvord Hot Spring, Antelope Hot Spring‐Hart Mountain, Borax Lake, Crump Geyser, and Mickey Hot Spring in southern Oregon. - Western Utah: Newcastle, Veyo Hot Spring, Dixie Hot Spring, Thermo, Roosevelt, Cove Fort, Red Hill Hot Spring, Joseph Hot Spring, Hatton Hot Spring, and Abraham‐Baker Hot Springs. Structural controls of 426 geothermal systems were analyzed with literature research, air photos, google‐Earth imagery, and/or field reviews (Figures 1 and 2). Of the systems analyzed, we were able to determine the structural settings of more than 240 sites. However, we found that many “systems” consisted of little more than a warm or hot well in the central part of a basin. Such “systems” were difficult to evaluate in terms of structural setting in areas lacking in geophysical data. Developed database for structural catalogue in a master spreadsheet. Data components include structural setting, primary fault orientation, presence or absence of Quaternary faulting, reservoir lithology, geothermometry, presence or absence of recent magmatism, and distinguishing blind systems from those that have surface expressions. Reviewed site locations for all 426 geothermal systems– Confirmed and/or relocated spring and geothermal sites based on imagery, maps, and other information for master database. Many systems were mislocated in the original database. In addition, some systems that included several separate springs spread over large areas were divided into two or more distinct systems. Further, all hot wells were assigned names based on their location to facilitate subsequent analyses. We catalogued systems into the following eight major groups, based on the dominant pattern of faulting (Figure 1): - Major normal fault segments (i.e., near displacement maxima). - Fault bends. - Fault terminations or tips. - Step‐overs or relay ramps in normal faults. - Fault intersections. - Accommodation zones (i.e., belts of intermeshing oppositely dipping normal faults), - Displacement transfer zones whereby strike‐slip faults terminate in arrays of normal faults. - Transtensional pull‐aparts. These settings form a hierarchal pattern with respect to fault complexity. - Major normal faults and fault bends are the simplest. - Fault terminations are typically more complex than mid‐segments, as faults commonly break up into multiple strands or horsetail near their ends. - A fault intersection is generally more complex, as it generally contains both multiple fault strands and can include discrete di...

U.S. Geological Survey coal quality (COALQUAL) database; version 2.0

USGS Publications Warehouse

Bragg, L.J.; Oman, J.K.; Tewalt, S.J.; Oman, C.L.; Rega, N.H.; Washington, P.M.; Finkelman, R.B.

1997-01-01

The USGS Coal Quality database is an interactive, computerized component of the NCRDS. It contains comprehensive analyses of more than 13,000 samples of coal and associated rocks from every major coal-bearing basin and coal bed in the U.S. The data in the coal quality database represent analyses of the coal as it exists in the ground. The data commonly are presented on an as-received whole-coal basis.

James Webb Space Telescope: Supporting Multiple Ground System Transitions in One Year

NASA Technical Reports Server (NTRS)

Detter, Ryan; Fatig, Curtis; Steck, Jane

2004-01-01

Ideas, requirements, and concepts developed during the very early phases of the mission design often conflict with the reality of a situation once the prime contractors are awarded. This happened for the James Webb Space Telescope (JWST) as well. The high level requirement of a common real-time ground system for both the Integration and Test (I&T), as well as the Operation phase of the mission is meant to reduce the cost and time needed later in the mission development for re-certification of databases, command and control systems, scripts, display pages, etc. In the case of JWST, the early Phase A flight software development needed a real-time ground system and database prior to the spacecraft prime contractor being selected. To compound the situation, the very low level requirements for the real-time ground system were not well defined. These two situations caused the initial real-time ground system to be switched out for a system that was previously used by the Bight software development team. To meet the high-!evel requirement, a third ground system was selected based on the prime spacecraft contractor needs and JWST Project decisions. The JWST ground system team has responded to each of these changes successfully. The lessons learned from each transition have not only made each transition smoother, but have also resolved issues earlier in the mission development than what would normally occur.

PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes

PubMed Central

Bhawna; Bonthala, V.S.; Gajula, MNV Prasad

2016-01-01

The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely. Database URL: http://www.multiomics.in/PvTFDB/ PMID:27465131

Feasibility and utility of applications of the common data model to multiple, disparate observational health databases

PubMed Central

Makadia, Rupa; Matcho, Amy; Ma, Qianli; Knoll, Chris; Schuemie, Martijn; DeFalco, Frank J; Londhe, Ajit; Zhu, Vivienne; Ryan, Patrick B

2015-01-01

Objectives To evaluate the utility of applying the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) across multiple observational databases within an organization and to apply standardized analytics tools for conducting observational research. Materials and methods Six deidentified patient-level datasets were transformed to the OMOP CDM. We evaluated the extent of information loss that occurred through the standardization process. We developed a standardized analytic tool to replicate the cohort construction process from a published epidemiology protocol and applied the analysis to all 6 databases to assess time-to-execution and comparability of results. Results Transformation to the CDM resulted in minimal information loss across all 6 databases. Patients and observations excluded were due to identified data quality issues in the source system, 96% to 99% of condition records and 90% to 99% of drug records were successfully mapped into the CDM using the standard vocabulary. The full cohort replication and descriptive baseline summary was executed for 2 cohorts in 6 databases in less than 1 hour. Discussion The standardization process improved data quality, increased efficiency, and facilitated cross-database comparisons to support a more systematic approach to observational research. Comparisons across data sources showed consistency in the impact of inclusion criteria, using the protocol and identified differences in patient characteristics and coding practices across databases. Conclusion Standardizing data structure (through a CDM), content (through a standard vocabulary with source code mappings), and analytics can enable an institution to apply a network-based approach to observational research across multiple, disparate observational health databases. PMID:25670757

Regulatory administrative databases in FDA's Center for Biologics Evaluation and Research: convergence toward a unified database.

PubMed

Smith, Jeffrey K

2013-04-01

Regulatory administrative database systems within the Food and Drug Administration's (FDA) Center for Biologics Evaluation and Research (CBER) are essential to supporting its core mission, as a regulatory agency. Such systems are used within FDA to manage information and processes surrounding the processing, review, and tracking of investigational and marketed product submissions. This is an area of increasing interest in the pharmaceutical industry and has been a topic at trade association conferences (Buckley 2012). Such databases in CBER are complex, not for the type or relevance of the data to any particular scientific discipline but because of the variety of regulatory submission types and processes the systems support using the data. Commonalities among different data domains of CBER's regulatory administrative databases are discussed. These commonalities have evolved enough to constitute real database convergence and provide a valuable asset for business process intelligence. Balancing review workload across staff, exploring areas of risk in review capacity, process improvement, and presenting a clear and comprehensive landscape of review obligations are just some of the opportunities of such intelligence. This convergence has been occurring in the presence of usual forces that tend to drive information technology (IT) systems development toward separate stovepipes and data silos. CBER has achieved a significant level of convergence through a gradual process, using a clear goal, agreed upon development practices, and transparency of database objects, rather than through a single, discrete project or IT vendor solution. This approach offers a path forward for FDA systems toward a unified database.

77 FR 42736 - Common Formats for Patient Safety Data Collection and Event Reporting

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-20

... Safety Databases (NPSD). Since the initial release of the Common Formats in August 2008, AHRQ has.... The inventory includes many systems from the private sector, including prominent academic settings...

Choosing an Optimal Database for Protein Identification from Tandem Mass Spectrometry Data.

PubMed

Kumar, Dhirendra; Yadav, Amit Kumar; Dash, Debasis

2017-01-01

Database searching is the preferred method for protein identification from digital spectra of mass to charge ratios (m/z) detected for protein samples through mass spectrometers. The search database is one of the major influencing factors in discovering proteins present in the sample and thus in deriving biological conclusions. In most cases the choice of search database is arbitrary. Here we describe common search databases used in proteomic studies and their impact on final list of identified proteins. We also elaborate upon factors like composition and size of the search database that can influence the protein identification process. In conclusion, we suggest that choice of the database depends on the type of inferences to be derived from proteomics data. However, making additional efforts to build a compact and concise database for a targeted question should generally be rewarding in achieving confident protein identifications.

A World Wide Web (WWW) server database engine for an organelle database, MitoDat.

PubMed

Lemkin, P F; Chipperfield, M; Merril, C; Zullo, S

1996-03-01

We describe a simple database search engine "dbEngine" which may be used to quickly create a searchable database on a World Wide Web (WWW) server. Data may be prepared from spreadsheet programs (such as Excel, etc.) or from tables exported from relationship database systems. This Common Gateway Interface (CGI-BIN) program is used with a WWW server such as available commercially, or from National Center for Supercomputer Algorithms (NCSA) or CERN. Its capabilities include: (i) searching records by combinations of terms connected with ANDs or ORs; (ii) returning search results as hypertext links to other WWW database servers; (iii) mapping lists of literature reference identifiers to the full references; (iv) creating bidirectional hypertext links between pictures and the database. DbEngine has been used to support the MitoDat database (Mendelian and non-Mendelian inheritance associated with the Mitochondrion) on the WWW.

Examining database persistence of ISO/EN 13606 standardized electronic health record extracts: relational vs. NoSQL approaches.

PubMed

Sánchez-de-Madariaga, Ricardo; Muñoz, Adolfo; Lozano-Rubí, Raimundo; Serrano-Balazote, Pablo; Castro, Antonio L; Moreno, Oscar; Pascual, Mario

2017-08-18

The objective of this research is to compare the relational and non-relational (NoSQL) database systems approaches in order to store, recover, query and persist standardized medical information in the form of ISO/EN 13606 normalized Electronic Health Record XML extracts, both in isolation and concurrently. NoSQL database systems have recently attracted much attention, but few studies in the literature address their direct comparison with relational databases when applied to build the persistence layer of a standardized medical information system. One relational and two NoSQL databases (one document-based and one native XML database) of three different sizes have been created in order to evaluate and compare the response times (algorithmic complexity) of six different complexity growing queries, which have been performed on them. Similar appropriate results available in the literature have also been considered. Relational and non-relational NoSQL database systems show almost linear algorithmic complexity query execution. However, they show very different linear slopes, the former being much steeper than the two latter. Document-based NoSQL databases perform better in concurrency than in isolation, and also better than relational databases in concurrency. Non-relational NoSQL databases seem to be more appropriate than standard relational SQL databases when database size is extremely high (secondary use, research applications). Document-based NoSQL databases perform in general better than native XML NoSQL databases. EHR extracts visualization and edition are also document-based tasks more appropriate to NoSQL database systems. However, the appropriate database solution much depends on each particular situation and specific problem.

Statistical characterization of a large geochemical database and effect of sample size

USGS Publications Warehouse

Zhang, C.; Manheim, F.T.; Hinde, J.; Grossman, J.N.

2005-01-01

The authors investigated statistical distributions for concentrations of chemical elements from the National Geochemical Survey (NGS) database of the U.S. Geological Survey. At the time of this study, the NGS data set encompasses 48,544 stream sediment and soil samples from the conterminous United States analyzed by ICP-AES following a 4-acid near-total digestion. This report includes 27 elements: Al, Ca, Fe, K, Mg, Na, P, Ti, Ba, Ce, Co, Cr, Cu, Ga, La, Li, Mn, Nb, Nd, Ni, Pb, Sc, Sr, Th, V, Y and Zn. The goal and challenge for the statistical overview was to delineate chemical distributions in a complex, heterogeneous data set spanning a large geographic range (the conterminous United States), and many different geological provinces and rock types. After declustering to create a uniform spatial sample distribution with 16,511 samples, histograms and quantile-quantile (Q-Q) plots were employed to delineate subpopulations that have coherent chemical and mineral affinities. Probability groupings are discerned by changes in slope (kinks) on the plots. Major rock-forming elements, e.g., Al, Ca, K and Na, tend to display linear segments on normal Q-Q plots. These segments can commonly be linked to petrologic or mineralogical associations. For example, linear segments on K and Na plots reflect dilution of clay minerals by quartz sand (low in K and Na). Minor and trace element relationships are best displayed on lognormal Q-Q plots. These sensitively reflect discrete relationships in subpopulations within the wide range of the data. For example, small but distinctly log-linear subpopulations for Pb, Cu, Zn and Ag are interpreted to represent ore-grade enrichment of naturally occurring minerals such as sulfides. None of the 27 chemical elements could pass the test for either normal or lognormal distribution on the declustered data set. Part of the reasons relate to the presence of mixtures of subpopulations and outliers. Random samples of the data set with successively smaller numbers of data points showed that few elements passed standard statistical tests for normality or log-normality until sample size decreased to a few hundred data points. Large sample size enhances the power of statistical tests, and leads to rejection of most statistical hypotheses for real data sets. For large sample sizes (e.g., n > 1000), graphical methods such as histogram, stem-and-leaf, and probability plots are recommended for rough judgement of probability distribution if needed. ?? 2005 Elsevier Ltd. All rights reserved.

Empty Sella Syndrome

MedlinePlus

... hormone prolactin, which can interfere with the normal function of the testicles and ovaries. Primary ESS is most common in adults and women, ... hormone prolactin, which can interfere with the normal function of the testicles and ovaries. Primary ESS is most common in adults and women, ...

A Full Snow Season in Yellowstone: A Database of Restored Aqua Band 6

NASA Technical Reports Server (NTRS)

Gladkova, Irina; Grossberg, Michael; Bonev, George; Romanov, Peter; Riggs, George; Hall, Dorothy

2013-01-01

The algorithms for estimating snow extent for the Moderate Resolution Imaging Spectroradiometer (MODIS) optimally use the 1.6- m channel which is unavailable for MODIS on Aqua due to detector damage. As a test bed to demonstrate that Aqua band 6 can be restored, we chose the area surrounding Yellowstone and Grand Teton national parks. In such rugged and difficult-to-access terrain, satellite images are particularly important for providing an estimation of snow-cover extent. For the full 2010-2011 snow season covering the Yellowstone region, we have used quantitative image restoration to create a database of restored Aqua band 6. The database includes restored radiances, normalized vegetation index, normalized snow index, thermal data, and band-6-based snow-map products. The restored Aqua-band-6 data have also been regridded and combined with Terra data to produce a snow-cover map that utilizes both Terra and Aqua snow maps. Using this database, we show that the restored Aqua-band-6-based snow-cover extent has a comparable performance with respect to ground stations to the one based on Terra. The result of a restored band 6 from Aqua is that we have an additional band-6 image of the Yellowstone region each day. This image can be used to mitigate cloud occlusion, using the same algorithms used for band 6 on Terra. We show an application of this database of restored band-6 images to illustrate the value of creating a cloud gap filling using the National Aeronautics and Space Administration s operational cloud masks and data from both Aqua and Terra.

Metabolic changes associated with papillary thyroid carcinoma: A nuclear magnetic resonance-based metabolomics study.

PubMed

Li, Yanyun; Chen, Minjian; Liu, Cuiping; Xia, Yankai; Xu, Bo; Hu, Yanhui; Chen, Ting; Shen, Meiping; Tang, Wei

2018-05-01

Papillary thyroid carcinoma (PTC) is the most common thyroid cancer. Nuclear magnetic resonance (NMR)‑based metabolomic technique is the gold standard in metabolite structural elucidation, and can provide different coverage of information compared with other metabolomic techniques. Here, we firstly conducted NMR based metabolomics study regarding detailed metabolic changes especially metabolic pathway changes related to PTC pathogenesis. 1H NMR-based metabolomic technique was adopted in conju-nction with multivariate analysis to analyze matched tumor and normal thyroid tissues obtained from 16 patients. The results were further annotated with Kyoto Encyclopedia of Genes and Genomes (KEGG), and Human Metabolome Database, and then were analyzed using modules of pathway analysis and enrichment analysis of MetaboAnalyst 3.0. Based on the analytical techniques, we established the models of principal component analysis (PCA), partial least squares-discriminant analysis (PLS-DA), and orthogonal partial least-squares discriminant analysis (OPLS‑DA) which could discriminate PTC from normal thyroid tissue, and found 15 robust differentiated metabolites from two OPLS-DA models. We identified 8 KEGG pathways and 3 pathways of small molecular pathway database which were significantly related to PTC by using pathway analysis and enrichment analysis, respectively, through which we identified metabolisms related to PTC including branched chain amino acid metabolism (leucine and valine), other amino acid metabolism (glycine and taurine), glycolysis (lactate), tricarboxylic acid cycle (citrate), choline metabolism (choline, ethanolamine and glycerolphosphocholine) and lipid metabolism (very-low‑density lipoprotein and low-density lipoprotein). In conclusion, the PTC was characterized with increased glycolysis and inhibited tricarboxylic acid cycle, increased oncogenic amino acids as well as abnormal choline and lipid metabolism. The findings in this study provide new insights into detailed metabolic changes of PTC, and hold great potential in the treatment of PTC.

Defining new criteria for selection of cell-based intestinal models using publicly available databases

PubMed Central

2012-01-01

Background The criteria for choosing relevant cell lines among a vast panel of available intestinal-derived lines exhibiting a wide range of functional properties are still ill-defined. The objective of this study was, therefore, to establish objective criteria for choosing relevant cell lines to assess their appropriateness as tumor models as well as for drug absorption studies. Results We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium. We have compared a panel of intestinal cell lines with patient-derived normal and tumor epithelium and classified them according to traits relating to oncogenic pathway activity, epithelial-mesenchymal transition (EMT) and stemness, migratory properties, proliferative activity, transporter expression profiles and chemosensitivity. For example, SW480 represent an EMT-high, migratory phenotype and scored highest in terms of signatures associated to worse overall survival and higher risk of recurrence based on patient derived databases. On the other hand, differentiated HT29 and T84 cells showed gene expression patterns closest to tumor bulk derived cells. Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine. Regarding chemosensitivity we were unable to confirm a recently proposed association of chemo-resistance with EMT traits. However, a novel signature was identified through mining of NCI60 GI50 values that allowed to rank the panel of intestinal cell lines according to their drug responsiveness to commonly used chemotherapeutics. Conclusions This study presents a straightforward strategy to exploit publicly available gene expression data to guide the choice of cell-based models. While this approach does not overcome the major limitations of such models, introducing a rank order of selected features may allow selecting model cell lines that are more adapted and pertinent to the addressed biological question. PMID:22726358

From Intensity Profile to Surface Normal: Photometric Stereo for Unknown Light Sources and Isotropic Reflectances.

PubMed

Lu, Feng; Matsushita, Yasuyuki; Sato, Imari; Okabe, Takahiro; Sato, Yoichi

2015-10-01

We propose an uncalibrated photometric stereo method that works with general and unknown isotropic reflectances. Our method uses a pixel intensity profile, which is a sequence of radiance intensities recorded at a pixel under unknown varying directional illumination. We show that for general isotropic materials and uniformly distributed light directions, the geodesic distance between intensity profiles is linearly related to the angular difference of their corresponding surface normals, and that the intensity distribution of the intensity profile reveals reflectance properties. Based on these observations, we develop two methods for surface normal estimation; one for a general setting that uses only the recorded intensity profiles, the other for the case where a BRDF database is available while the exact BRDF of the target scene is still unknown. Quantitative and qualitative evaluations are conducted using both synthetic and real-world scenes, which show the state-of-the-art accuracy of smaller than 10 degree without using reference data and 5 degree with reference data for all 100 materials in MERL database.

EPA Treatability Database Digs Deep for Data on Drinking Water Contaminants and Treatment Processes

EPA Science Inventory

The TDB is an interactive database that was initially developed in 2006-2007. The TDB currently contains more than 60 regulated and unregulated contaminants and 28 treatment processes that are known to be effective and are commonly employed at drinking water utilities. TDB lite...

Transportation-markings database : railway signals, signs, marks and markers. Part I 3, Volume 3, additional studies

DOT National Transportation Integrated Search

2009-01-01

The Database demonstrates the unity and commonality of T-M but presents each one in its separate state. Yet in that process the full panopoly of T-M is unfolded including their shared and connected state. There are thousands of Trasportation-Markings...

Customizable tool for ecological data entry, assessment, monitoring, and interpretation

USDA-ARS?s Scientific Manuscript database

The Database for Inventory, Monitoring and Assessment (DIMA) is a highly customizable tool for data entry, assessment, monitoring, and interpretation. DIMA is a Microsoft Access database that can easily be used without Access knowledge and is available at no cost. Data can be entered for common, nat...

Taste Perception: An Examination of Fat Preference, Sensory Specific Satiety, and the Function of Eating Among Moderately Obese and Normal Weight Women

DTIC Science & Technology

2001-02-20

key will take you into the food database so you can find the specific type of food you have eaten. For example if you ate a roasted chicken breast...you would type in chicken , press the Enter key and then press an arrow key to locate chicken , breast, meat only, roasted in the food database...Taste Perception 61 Appendix B: Pudding Recipes High fat pudding

Acoustic fill factors for a 120 inch diameter fairing

NASA Technical Reports Server (NTRS)

Lee, Y. Albert

1992-01-01

Data from the acoustic test of a 120-inch diameter payload fairing were collected and an analysis of acoustic fill factors were performed. Correction factors for obtaining a weighted spatial average of the interior sound pressure level (SPL) were derived based on this database and a normalized 200-inch diameter fairing database. The weighted fill factors were determined and compared with statistical energy analysis (VAPEPS code) derived fill factors. The comparison is found to be reasonable.

A functional-dependencies-based Bayesian networks learning method and its application in a mobile commerce system.

PubMed

Liao, Stephen Shaoyi; Wang, Huai Qing; Li, Qiu Dan; Liu, Wei Yi

2006-06-01

This paper presents a new method for learning Bayesian networks from functional dependencies (FD) and third normal form (3NF) tables in relational databases. The method sets up a linkage between the theory of relational databases and probabilistic reasoning models, which is interesting and useful especially when data are incomplete and inaccurate. The effectiveness and practicability of the proposed method is demonstrated by its implementation in a mobile commerce system.

Determining conserved metabolic biomarkers from a million database queries.

PubMed

Kurczy, Michael E; Ivanisevic, Julijana; Johnson, Caroline H; Uritboonthai, Winnie; Hoang, Linh; Fang, Mingliang; Hicks, Matthew; Aldebot, Anthony; Rinehart, Duane; Mellander, Lisa J; Tautenhahn, Ralf; Patti, Gary J; Spilker, Mary E; Benton, H Paul; Siuzdak, Gary

2015-12-01

Metabolite databases provide a unique window into metabolome research allowing the most commonly searched biomarkers to be catalogued. Omic scale metabolite profiling, or metabolomics, is finding increased utility in biomarker discovery largely driven by improvements in analytical technologies and the concurrent developments in bioinformatics. However, the successful translation of biomarkers into clinical or biologically relevant indicators is limited. With the aim of improving the discovery of translatable metabolite biomarkers, we present search analytics for over one million METLIN metabolite database queries. The most common metabolites found in METLIN were cross-correlated against XCMS Online, the widely used cloud-based data processing and pathway analysis platform. Analysis of the METLIN and XCMS common metabolite data has two primary implications: these metabolites, might indicate a conserved metabolic response to stressors and, this data may be used to gauge the relative uniqueness of potential biomarkers. METLIN can be accessed by logging on to: https://metlin.scripps.edu siuzdak@scripps.edu Supplementary data are available at Bioinformatics online. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

CyanoClust: comparative genome resources of cyanobacteria and plastids.

PubMed

Sasaki, Naobumi V; Sato, Naoki

2010-01-01

Cyanobacteria, which perform oxygen-evolving photosynthesis as do chloroplasts of plants and algae, are one of the best-studied prokaryotic phyla and one from which many representative genomes have been sequenced. Lack of a suitable comparative genomic database has been a problem in cyanobacterial genomics because many proteins involved in physiological functions such as photosynthesis and nitrogen fixation are not catalogued in commonly used databases, such as Clusters of Orthologous Proteins (COG). CyanoClust is a database of homolog groups in cyanobacteria and plastids that are produced by the program Gclust. We have developed a web-server system for the protein homology database featuring cyanobacteria and plastids. Database URL: http://cyanoclust.c.u-tokyo.ac.jp/.

Landscape features, standards, and semantics in U.S. national topographic mapping databases

USGS Publications Warehouse

Varanka, Dalia

2009-01-01

The objective of this paper is to examine the contrast between local, field-surveyed topographical representation and feature representation in digital, centralized databases and to clarify their ontological implications. The semantics of these two approaches are contrasted by examining the categorization of features by subject domains inherent to national topographic mapping. When comparing five USGS topographic mapping domain and feature lists, results indicate that multiple semantic meanings and ontology rules were applied to the initial digital database, but were lost as databases became more centralized at national scales, and common semantics were replaced by technological terms.

Cervical spine alignment in the pediatric population: a radiographic normative study of 150 asymptomatic patients.

PubMed

Abelin-Genevois, K; Idjerouidene, A; Roussouly, P; Vital, J M; Garin, C

2014-07-01

To describe the normal cervical sagittal alignment of the pediatric spine in a normal population and to identify the changes during growth period. We randomly selected in PACS database 150 full-spine standing views. Exclusion criteria were: age >18 years, spinal deformity and any disease affecting the spine (medical charts reviewing). For cervical alignment we measured: OC-angle according to Mc Gregor, C1C7 angle, upper cervical angle, inferior cervical angle and C7 tilt. Spino pelvic parameters were analyzed: T1 tilt, thoracic kyphosis, lumbar lordosis, pelvic incidence, sacral slope and pelvic tilt. We compared two age subgroups (juvenile and adolescent). Differences between age groups and gender were tested using Student's t test. Correlations between sagittal spinal parameters were evaluated using Pearson's test. Cervical spine shape was correlated to cranio cervical orientation to maintain horizontal gaze (r = 0.60) and to thoracic kyphosis (r = -0.46). Cervical spine alignment was significantly different between the two age groups except for the global C1C7 cervical lordosis, which remained stable. A significant gender difference was found for all the cervical sagittal angles (p < 0.01) whereas no differences were demonstrated for the spino pelvic parameters, except the lumbar lordosis (p = 0.047). This study is the first to report the cervical spinal alignment in a normal pediatric Caucasian population. Even though cervical lordosis is the common shape, our results showed variability in cervical sagittal alignment. Cervical spine is a junctional area that adjusts its alignment to the head position and to the underlying spinal alignment.

Comparison of Cortical and Subcortical Measurements in Normal Older Adults across Databases and Software Packages

PubMed Central

Rane, Swati; Plassard, Andrew; Landman, Bennett A.; Claassen, Daniel O.; Donahue, Manus J.

2017-01-01

This work explores the feasibility of combining anatomical MRI data across two public repositories namely, the Alzheimer’s Disease Neuroimaging Initiative (ADNI) and the Progressive Parkinson’s Markers Initiative (PPMI). We compared cortical thickness and subcortical volumes in cognitively normal older adults between datasets with distinct imaging parameters to assess if they would provide equivalent information. Three distinct datasets were identified. Major differences in data were scanner manufacturer and the use of magnetization inversion to enhance tissue contrast. Equivalent datasets, i.e., those providing similar volumetric measurements in cognitively normal controls, were identified in ADNI and PPMI. These were datasets obtained on the Siemens scanner with TI = 900 ms. Our secondary goal was to assess the agreement between subcortical volumes that are obtained with different software packages. Three subcortical measurement applications (FSL, FreeSurfer, and a recent multi-atlas approach) were compared. Our results show significant agreement in the measurements of caudate, putamen, pallidum, and hippocampus across the packages and poor agreement between measurements of accumbens and amygdala. This is likely due to their smaller size and lack of gray matter-white matter tissue contrast for accurate segmentation. This work provides a segue to combine imaging data from ADNI and PPMI to increase statistical power as well as to interrogate common mechanisms in disparate pathologies such as Alzheimer’s and Parkinson’s diseases. It lays the foundation for comparison of anatomical data acquired with disparate imaging parameters and analyzed with disparate software tools. Furthermore, our work partly explains the variability in the results of studies using different software packages. PMID:29756095

Comparison of Cortical and Subcortical Measurements in Normal Older Adults across Databases and Software Packages.

PubMed

Rane, Swati; Plassard, Andrew; Landman, Bennett A; Claassen, Daniel O; Donahue, Manus J

2017-01-01

This work explores the feasibility of combining anatomical MRI data across two public repositories namely, the Alzheimer's Disease Neuroimaging Initiative (ADNI) and the Progressive Parkinson's Markers Initiative (PPMI). We compared cortical thickness and subcortical volumes in cognitively normal older adults between datasets with distinct imaging parameters to assess if they would provide equivalent information. Three distinct datasets were identified. Major differences in data were scanner manufacturer and the use of magnetization inversion to enhance tissue contrast. Equivalent datasets, i.e., those providing similar volumetric measurements in cognitively normal controls, were identified in ADNI and PPMI. These were datasets obtained on the Siemens scanner with TI = 900 ms. Our secondary goal was to assess the agreement between subcortical volumes that are obtained with different software packages. Three subcortical measurement applications (FSL, FreeSurfer, and a recent multi-atlas approach) were compared. Our results show significant agreement in the measurements of caudate, putamen, pallidum, and hippocampus across the packages and poor agreement between measurements of accumbens and amygdala. This is likely due to their smaller size and lack of gray matter-white matter tissue contrast for accurate segmentation. This work provides a segue to combine imaging data from ADNI and PPMI to increase statistical power as well as to interrogate common mechanisms in disparate pathologies such as Alzheimer's and Parkinson's diseases. It lays the foundation for comparison of anatomical data acquired with disparate imaging parameters and analyzed with disparate software tools. Furthermore, our work partly explains the variability in the results of studies using different software packages.

SQLGEN: a framework for rapid client-server database application development.

PubMed

Nadkarni, P M; Cheung, K H

1995-12-01

SQLGEN is a framework for rapid client-server relational database application development. It relies on an active data dictionary on the client machine that stores metadata on one or more database servers to which the client may be connected. The dictionary generates dynamic Structured Query Language (SQL) to perform common database operations; it also stores information about the access rights of the user at log-in time, which is used to partially self-configure the behavior of the client to disable inappropriate user actions. SQLGEN uses a microcomputer database as the client to store metadata in relational form, to transiently capture server data in tables, and to allow rapid application prototyping followed by porting to client-server mode with modest effort. SQLGEN is currently used in several production biomedical databases.

A Generic Data Harmonization Process for Cross-linked Research and Network Interaction. Construction and Application for the Lung Cancer Phenotype Database of the German Center for Lung Research.

PubMed

Firnkorn, D; Ganzinger, M; Muley, T; Thomas, M; Knaup, P

2015-01-01

Joint data analysis is a key requirement in medical research networks. Data are available in heterogeneous formats at each network partner and their harmonization is often rather complex. The objective of our paper is to provide a generic approach for the harmonization process in research networks. We applied the process when harmonizing data from three sites for the Lung Cancer Phenotype Database within the German Center for Lung Research. We developed a spreadsheet-based solution as tool to support the harmonization process for lung cancer data and a data integration procedure based on Talend Open Studio. The harmonization process consists of eight steps describing a systematic approach for defining and reviewing source data elements and standardizing common data elements. The steps for defining common data elements and harmonizing them with local data definitions are repeated until consensus is reached. Application of this process for building the phenotype database led to a common basic data set on lung cancer with 285 structured parameters. The Lung Cancer Phenotype Database was realized as an i2b2 research data warehouse. Data harmonization is a challenging task requiring informatics skills as well as domain knowledge. Our approach facilitates data harmonization by providing guidance through a uniform process that can be applied in a wide range of projects.

Malpractice in treatment of sinonasal disease by otolaryngologists: a review of the past 10 years.

PubMed

Winford, Tyler W; Wallin, Jordan L; Clinger, John D; Graham, Aaron M

2015-03-01

Sinonasal disease is a common condition treated by otolaryngologists. Malpractice in this area is the most common litigation faced by otolaryngologists. This study analyzes malpractice in the treatment of sinonasal disease. Case series, review of legal records. Legal databases. Using 2 different computerized legal databases, the phrase medical malpractice was searched with terms related to sinonasal disease involving court cases in the past 10 years (2004-2013), yielding 26 cases. The cases were analyzed for pertinent data regarding plaintiffs, presenting complaint, practice setting, type of malpractice, resulting injury, result of verdict, and amount of reward or settlement. Chronic sinusitis (42%) was the most common presenting symptom. Many cases included multiple types of alleged malpractice, with the most common being negligent technique (38%) and lack of informed consent (27%). The most common alleged injuries included cerebrospinal fluid leak, meningitis, nasal obstruction, and orbital trauma. Defendants prevailed in 13 of 18 cases in which outcomes were known, with mean award of $225,000 and mean settlement of $212,500. The cases won by plaintiffs were all in a private practice setting. Otolaryngologists should be aware of the causes of malpractice litigation as it relates to treatment of sinonasal disease. Lack of informed consent continues to be a common allegation, and surgeons should ensure complete informed consent is obtained and well documented. A unified and complete database of medical malpractice cases is needed to allow for further analysis of specialty-related claims. © American Academy of Otolaryngology—Head and Neck Surgery Foundation 2015.

The Government Finance Database: A Common Resource for Quantitative Research in Public Financial Analysis

PubMed Central

Pierson, Kawika; Hand, Michael L.; Thompson, Fred

2015-01-01

Quantitative public financial management research focused on local governments is limited by the absence of a common database for empirical analysis. While the U.S. Census Bureau distributes government finance data that some scholars have utilized, the arduous process of collecting, interpreting, and organizing the data has led its adoption to be prohibitive and inconsistent. In this article we offer a single, coherent resource that contains all of the government financial data from 1967-2012, uses easy to understand natural-language variable names, and will be extended when new data is available. PMID:26107821

The Government Finance Database: A Common Resource for Quantitative Research in Public Financial Analysis.

PubMed

Pierson, Kawika; Hand, Michael L; Thompson, Fred

2015-01-01

Quantitative public financial management research focused on local governments is limited by the absence of a common database for empirical analysis. While the U.S. Census Bureau distributes government finance data that some scholars have utilized, the arduous process of collecting, interpreting, and organizing the data has led its adoption to be prohibitive and inconsistent. In this article we offer a single, coherent resource that contains all of the government financial data from 1967-2012, uses easy to understand natural-language variable names, and will be extended when new data is available.

Menstrual physiology: implications for endometrial pathology and beyond

PubMed Central

Maybin, Jacqueline A.; Critchley, Hilary O.D.

2015-01-01

BACKGROUND Each month the endometrium becomes inflamed, and the luminal portion is shed during menstruation. The subsequent repair is remarkable, allowing implantation to occur if fertilization takes place. Aberrations in menstrual physiology can lead to common gynaecological conditions, such as heavy or prolonged bleeding. Increased knowledge of the processes involved in menstrual physiology may also have translational benefits at other tissue sites. METHODS Pubmed and Cochrane databases were searched for all original and review articles published in English until April 2015. Search terms included ‘endometrium’, ‘menstruation’, ‘endometrial repair’, ‘endometrial regeneration’ ‘angiogenesis’, ‘inflammation’ and ‘heavy menstrual bleeding’ or ‘menorrhagia’. RESULTS Menstruation occurs naturally in very few species. Human menstruation is thought to occur as a consequence of preimplantation decidualization, conferring embryo selectivity and the ability to adapt to optimize function. We highlight how current and future study of endometrial inflammation, vascular changes and repair/regeneration will allow us to identify new therapeutic targets for common gynaecological disorders. In addition, we describe how increased knowledge of this endometrial physiology will have many translational applications at other tissue sites. We highlight the clinical applications of what we know, the key questions that remain and the scientific and medical possibilities for the future. CONCLUSIONS The study of menstruation, in both normal and abnormal scenarios, is essential for the production of novel, acceptable medical treatments for common gynaecological complaints. Furthermore, collaboration and communication with specialists in other fields could significantly advance the therapeutic potential of this dynamic tissue. PMID:26253932

Proteomic and Bioinformatic Profile of Primary Human Oral Epithelial Cells

PubMed Central

Ghosh, Santosh K.; Yohannes, Elizabeth; Bebek, Gurkan; Weinberg, Aaron; Jiang, Bin; Willard, Belinda; Chance, Mark R.; Kinter, Michael T.; McCormick, Thomas S.

2012-01-01

Wounding of the oral mucosa occurs frequently in a highly septic environment. Remarkably, these wounds heal quickly and the oral cavity, for the most part, remains healthy. Deciphering the normal human oral epithelial cell (NHOEC) proteome is critical for understanding the mechanism(s) of protection elicited when the mucosal barrier is intact, as well as when it is breached. Combining 2D gel electrophoresis with shotgun proteomics resulted in identification of 1662 NHOEC proteins. Proteome annotations were performed based on protein classes, molecular functions, disease association and membership in canonical and metabolic signaling pathways. Comparing the NHOEC proteome with a database of innate immunity-relevant interactions (InnateDB) identified 64 common proteins associated with innate immunity. Comparison with published salivary proteomes revealed that 738/1662 NHOEC proteins were common, suggesting that significant numbers of salivary proteins are of epithelial origin. Gene ontology analysis showed similarities in the distributions of NHOEC and saliva proteomes with regard to biological processes, and molecular functions. We also assessed the inter-individual variability of the NHOEC proteome and observed it to be comparable with other primary cells. The baseline proteome described in this study should serve as a resource for proteome studies of the oral mucosa, especially in relation to disease processes. PMID:23035736

The contribution of reinforcement sensitivity to the personality-psychopathology hierarchical structure in childhood and adolescence.

PubMed

Slobodskaya, Helena R

2016-11-01

This study examined the contribution of reinforcement sensitivity to the hierarchical structure of child personality and common psychopathology in community samples of parent reports of children aged 2-18 (N = 968) and self-reports of adolescents aged 10-18 (N = 1,543) using the Inventory of Child Individual Differences-Short version (ICID-S), the Strengths and Difficulties Questionnaire (SDQ), and the Sensitivity to Punishment and Sensitivity to Reward Questionnaire (SPSRQ). A joint higher-order factor analysis of the ICID-S and SDQ scales suggested a 4-factor solution; congruence coefficients indicated replicability of the factors across the 2 samples at all levels of the personality-psychopathology hierarchy. The canonical correlation analyses indicated that reinforcement sensitivity and personality-psychopathology dimensions shared much of their variance. The main contribution of reinforcement sensitivity was through opposing effects of reward and punishment sensitivities. The superordinate factors Beta and Internalizing were best predicted by reinforcement sensitivity, followed by the Externalizing and Positive personality factors. These findings provide evidence for consistency of the hierarchical structure of personality and common psychopathology across informants and highlight the role of reinforcement systems in the development of normal and abnormal patterns of behavior and affect. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Understanding Expenditure Data.

ERIC Educational Resources Information Center

Dyke, Frances L.

2000-01-01

Stresses the importance of common understandings of cost definitions and data collection in order to create reliable databases with optimal utility for inter-institutional analysis. Examines definitions of common expenditure categories, discusses cost-accumulation rules governing financial reporting, and explains differences between direct costs…

A database for estimating organ dose for coronary angiography and brain perfusion CT scans for arbitrary spectra and angular tube current modulation

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

Rupcich, Franco; Badal, Andreu; Kyprianou, Iacovos

Purpose: The purpose of this study was to develop a database for estimating organ dose in a voxelized patient model for coronary angiography and brain perfusion CT acquisitions with any spectra and angular tube current modulation setting. The database enables organ dose estimation for existing and novel acquisition techniques without requiring Monte Carlo simulations. Methods: The study simulated transport of monoenergetic photons between 5 and 150 keV for 1000 projections over 360 Degree-Sign through anthropomorphic voxelized female chest and head (0 Degree-Sign and 30 Degree-Sign tilt) phantoms and standard head and body CTDI dosimetry cylinders. The simulations resulted in tablesmore » of normalized dose deposition for several radiosensitive organs quantifying the organ dose per emitted photon for each incident photon energy and projection angle for coronary angiography and brain perfusion acquisitions. The values in a table can be multiplied by an incident spectrum and number of photons at each projection angle and then summed across all energies and angles to estimate total organ dose. Scanner-specific organ dose may be approximated by normalizing the database-estimated organ dose by the database-estimated CTDI{sub vol} and multiplying by a physical CTDI{sub vol} measurement. Two examples are provided demonstrating how to use the tables to estimate relative organ dose. In the first, the change in breast and lung dose during coronary angiography CT scans is calculated for reduced kVp, angular tube current modulation, and partial angle scanning protocols relative to a reference protocol. In the second example, the change in dose to the eye lens is calculated for a brain perfusion CT acquisition in which the gantry is tilted 30 Degree-Sign relative to a nontilted scan. Results: Our database provides tables of normalized dose deposition for several radiosensitive organs irradiated during coronary angiography and brain perfusion CT scans. Validation results indicate total organ doses calculated using our database are within 1% of those calculated using Monte Carlo simulations with the same geometry and scan parameters for all organs except red bone marrow (within 6%), and within 23% of published estimates for different voxelized phantoms. Results from the example of using the database to estimate organ dose for coronary angiography CT acquisitions show 2.1%, 1.1%, and -32% change in breast dose and 2.1%, -0.74%, and 4.7% change in lung dose for reduced kVp, tube current modulated, and partial angle protocols, respectively, relative to the reference protocol. Results show -19.2% difference in dose to eye lens for a tilted scan relative to a nontilted scan. The reported relative changes in organ doses are presented without quantification of image quality and are for the sole purpose of demonstrating the use of the proposed database. Conclusions: The proposed database and calculation method enable the estimation of organ dose for coronary angiography and brain perfusion CT scans utilizing any spectral shape and angular tube current modulation scheme by taking advantage of the precalculated Monte Carlo simulation results. The database can be used in conjunction with image quality studies to develop optimized acquisition techniques and may be particularly beneficial for optimizing dual kVp acquisitions for which numerous kV, mA, and filtration combinations may be investigated.« less

Computed Tomography of the Abdomen in Eight Clinically Normal Common Marmosets (Callithrix jacchus).

PubMed

du Plessis, W M; Groenewald, H B; Elliott, D

2017-08-01

The aim of this study was to provide a detailed anatomical description of the abdomen in the clinically normal common marmoset by means of computed tomography (CT). Eight clinically healthy mature common marmosets ranging from 12 to 48 months and 235 to 365 g bodyweight were anesthetized and pre- and post-contrast CT examinations were performed using different CT settings in dorsal recumbency. Abdominal organs were identified and visibility noted. Diagnostic quality abdominal images could be obtained of the common marmoset despite its small size using a dual-slice CT scanner. Representative cross-sectional images were chosen from different animals illustrating the abdominal CT anatomy of clinically normal common marmosets. Identification or delineation of abdominal organs greatly improved with i.v. contrast. A modified high-frequency algorithm with edge enhancement added valuable information for identification of small structures such as the ureters. The Hounsfield unit (HU) of major abdominal organs differed from that of small animals (domestic dogs and cats). Due to their size and different anatomy, standard small animal CT protocols need to be critically assessed and adapted for exotics, such as the common marmoset. The established normal reference range of HU of major abdominal organs and adapted settings for a CT protocol will aid clinical assessment of the common marmoset. © 2017 Blackwell Verlag GmbH.

Understanding a Normal Distribution of Data.

PubMed

Maltenfort, Mitchell G

2015-12-01

Assuming data follow a normal distribution is essential for many common statistical tests. However, what are normal data and when can we assume that a data set follows this distribution? What can be done to analyze non-normal data?

Heterogeneous distributed databases: A case study

NASA Technical Reports Server (NTRS)

Stewart, Tracy R.; Mukkamala, Ravi

1991-01-01

Alternatives are reviewed for accessing distributed heterogeneous databases and a recommended solution is proposed. The current study is limited to the Automated Information Systems Center at the Naval Sea Combat Systems Engineering Station at Norfolk, VA. This center maintains two databases located on Digital Equipment Corporation's VAX computers running under the VMS operating system. The first data base, ICMS, resides on a VAX11/780 and has been implemented using VAX DBMS, a CODASYL based system. The second database, CSA, resides on a VAX 6460 and has been implemented using the ORACLE relational database management system (RDBMS). Both databases are used for configuration management within the U.S. Navy. Different customer bases are supported by each database. ICMS tracks U.S. Navy ships and major systems (anti-sub, sonar, etc.). Even though the major systems on ships and submarines have totally different functions, some of the equipment within the major systems are common to both ships and submarines.

Applying AN Object-Oriented Database Model to a Scientific Database Problem: Managing Experimental Data at Cebaf.

NASA Astrophysics Data System (ADS)

Ehlmann, Bryon K.

Current scientific experiments are often characterized by massive amounts of very complex data and the need for complex data analysis software. Object-oriented database (OODB) systems have the potential of improving the description of the structure and semantics of this data and of integrating the analysis software with the data. This dissertation results from research to enhance OODB functionality and methodology to support scientific databases (SDBs) and, more specifically, to support a nuclear physics experiments database for the Continuous Electron Beam Accelerator Facility (CEBAF). This research to date has identified a number of problems related to the practical application of OODB technology to the conceptual design of the CEBAF experiments database and other SDBs: the lack of a generally accepted OODB design methodology, the lack of a standard OODB model, the lack of a clear conceptual level in existing OODB models, and the limited support in existing OODB systems for many common object relationships inherent in SDBs. To address these problems, the dissertation describes an Object-Relationship Diagram (ORD) and an Object-oriented Database Definition Language (ODDL) that provide tools that allow SDB design and development to proceed systematically and independently of existing OODB systems. These tools define multi-level, conceptual data models for SDB design, which incorporate a simple notation for describing common types of relationships that occur in SDBs. ODDL allows these relationships and other desirable SDB capabilities to be supported by an extended OODB system. A conceptual model of the CEBAF experiments database is presented in terms of ORDs and the ODDL to demonstrate their functionality and use and provide a foundation for future development of experimental nuclear physics software using an OODB approach.

Feasibility and utility of applications of the common data model to multiple, disparate observational health databases.

PubMed

Voss, Erica A; Makadia, Rupa; Matcho, Amy; Ma, Qianli; Knoll, Chris; Schuemie, Martijn; DeFalco, Frank J; Londhe, Ajit; Zhu, Vivienne; Ryan, Patrick B

2015-05-01

To evaluate the utility of applying the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) across multiple observational databases within an organization and to apply standardized analytics tools for conducting observational research. Six deidentified patient-level datasets were transformed to the OMOP CDM. We evaluated the extent of information loss that occurred through the standardization process. We developed a standardized analytic tool to replicate the cohort construction process from a published epidemiology protocol and applied the analysis to all 6 databases to assess time-to-execution and comparability of results. Transformation to the CDM resulted in minimal information loss across all 6 databases. Patients and observations excluded were due to identified data quality issues in the source system, 96% to 99% of condition records and 90% to 99% of drug records were successfully mapped into the CDM using the standard vocabulary. The full cohort replication and descriptive baseline summary was executed for 2 cohorts in 6 databases in less than 1 hour. The standardization process improved data quality, increased efficiency, and facilitated cross-database comparisons to support a more systematic approach to observational research. Comparisons across data sources showed consistency in the impact of inclusion criteria, using the protocol and identified differences in patient characteristics and coding practices across databases. Standardizing data structure (through a CDM), content (through a standard vocabulary with source code mappings), and analytics can enable an institution to apply a network-based approach to observational research across multiple, disparate observational health databases. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

PvTFDB: a Phaseolus vulgaris transcription factors database for expediting functional genomics in legumes.

PubMed

Bhawna; Bonthala, V S; Gajula, Mnv Prasad

2016-01-01

The common bean [Phaseolus vulgaris (L.)] is one of the essential proteinaceous vegetables grown in developing countries. However, its production is challenged by low yields caused by numerous biotic and abiotic stress conditions. Regulatory transcription factors (TFs) symbolize a key component of the genome and are the most significant targets for producing stress tolerant crop and hence functional genomic studies of these TFs are important. Therefore, here we have constructed a web-accessible TFs database for P. vulgaris, called PvTFDB, which contains 2370 putative TF gene models in 49 TF families. This database provides a comprehensive information for each of the identified TF that includes sequence data, functional annotation, SSRs with their primer sets, protein physical properties, chromosomal location, phylogeny, tissue-specific gene expression data, orthologues, cis-regulatory elements and gene ontology (GO) assignment. Altogether, this information would be used in expediting the functional genomic studies of a specific TF(s) of interest. The objectives of this database are to understand functional genomics study of common bean TFs and recognize the regulatory mechanisms underlying various stress responses to ease breeding strategy for variety production through a couple of search interfaces including gene ID, functional annotation and browsing interfaces including by family and by chromosome. This database will also serve as a promising central repository for researchers as well as breeders who are working towards crop improvement of legume crops. In addition, this database provide the user unrestricted public access and the user can download entire data present in the database freely.Database URL: http://www.multiomics.in/PvTFDB/. © The Author(s) 2016. Published by Oxford University Press.

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.

Databases in the Central Government : State-of-the-art and the Future

NASA Astrophysics Data System (ADS)

Ohashi, Tomohiro

Management and Coordination Agency, Prime Minister’s Office, conducted a survey by questionnaire against all Japanese Ministries and Agencies, in November 1985, on a subject of the present status of databases produced or planned to be produced by the central government. According to the results, the number of the produced databases has been 132 in 19 Ministries and Agencies. Many of such databases have been possessed by Defence Agency, Ministry of Construction, Ministry of Agriculture, Forestry & Fisheries, and Ministry of International Trade & Industries and have been in the fields of architecture & civil engineering, science & technology, R & D, agriculture, forestry and fishery. However the ratio of the databases available for other Ministries and Agencies has amounted to only 39 percent of all produced databases and the ratio of the databases unavailable for them has amounted to 60 percent of all of such databases, because of in-house databases and so forth. The outline of such results of the survey is reported and the databases produced by the central government are introduced under the items of (1) databases commonly used by all Ministries and Agencies, (2) integrated databases, (3) statistical databases and (4) bibliographic databases. The future problems are also described from the viewpoints of technology developments and mutual uses of databases.

Comparing IndexedHBase and Riak for Serving Truthy: Performance of Data Loading and Query Evaluation

DTIC Science & Technology

2013-08-01

Research Triangle Park, NC 27709-2211 15. SUBJECT TERMS performance evaluation, distributed database, noSQL , HBase, indexing Xiaoming Gao, Judy Qiu...common hashtags created during a given time window. With the purpose of finding a solution for these challenges, we evaluate NoSQL databases such as

"There's so Much Data": Exploring the Realities of Data-Based School Governance

ERIC Educational Resources Information Center

Selwyn, Neil

2016-01-01

Educational governance is commonly predicated around the generation, collation and processing of data through digital technologies. Drawing upon an empirical study of two Australian secondary schools, this paper explores the different forms of data-based governance that are being enacted by school leaders, managers, administrators and teachers.…

Conducting Survey Research via the Internet.

ERIC Educational Resources Information Center

Rice, Margaret L.; Wright, Vivian H.; Cofield, Jay; Stokes, Suzanne P.; Wilson, Elizabeth K.

This guide to creating a survey to be administered on the Internet used Microsoft Access as the database program for the illustration. Forty-four steps in constructing the survey, including the Common Gateway Interface that moves the data collected in e-mails directly to the database, are outlined. The example developed by researchers at the…

Sentence-Based Metadata: An Approach and Tool for Viewing Database Designs.

ERIC Educational Resources Information Center

Boyle, John M.; Gunge, Jakob; Bryden, John; Librowski, Kaz; Hanna, Hsin-Yi

2002-01-01

Describes MARS (Museum Archive Retrieval System), a research tool which enables organizations to exchange digital images and documents by means of a common thesaurus structure, and merge the descriptive data and metadata of their collections. Highlights include theoretical basis; searching the MARS database; and examples in European museums.…

Successful Keyword Searching: Initiating Research on Popular Topics Using Electronic Databases.

ERIC Educational Resources Information Center

MacDonald, Randall M.; MacDonald, Susan Priest

Students are using electronic resources more than ever before to locate information for assignments. Without the proper search terms, results are incomplete, and students are frustrated. Using the keywords, key people, organizations, and Web sites provided in this book and compiled from the most commonly used databases, students will be able to…

Complex Adaptive Systems Based Data Integration: Theory and Applications

ERIC Educational Resources Information Center

Rohn, Eliahu

2008-01-01

Data Definition Languages (DDLs) have been created and used to represent data in programming languages and in database dictionaries. This representation includes descriptions in the form of data fields and relations in the form of a hierarchy, with the common exception of relational databases where relations are flat. Network computing created an…

Analysis of Institutionally Specific Retention Research: A Comparison between Survey and Institutional Database Methods

ERIC Educational Resources Information Center

Caison, Amy L.

2007-01-01

This study empirically explores the comparability of traditional survey-based retention research methodology with an alternative approach that relies on data commonly available in institutional student databases. Drawing on Tinto's [Tinto, V. (1993). "Leaving College: Rethinking the Causes and Cures of Student Attrition" (2nd Ed.), The University…

Common hyperspectral image database design

NASA Astrophysics Data System (ADS)

Tian, Lixun; Liao, Ningfang; Chai, Ali

2009-11-01

This paper is to introduce Common hyperspectral image database with a demand-oriented Database design method (CHIDB), which comprehensively set ground-based spectra, standardized hyperspectral cube, spectral analysis together to meet some applications. The paper presents an integrated approach to retrieving spectral and spatial patterns from remotely sensed imagery using state-of-the-art data mining and advanced database technologies, some data mining ideas and functions were associated into CHIDB to make it more suitable to serve in agriculture, geological and environmental areas. A broad range of data from multiple regions of the electromagnetic spectrum is supported, including ultraviolet, visible, near-infrared, thermal infrared, and fluorescence. CHIDB is based on dotnet framework and designed by MVC architecture including five main functional modules: Data importer/exporter, Image/spectrum Viewer, Data Processor, Parameter Extractor, and On-line Analyzer. The original data were all stored in SQL server2008 for efficient search, query and update, and some advance Spectral image data Processing technology are used such as Parallel processing in C#; Finally an application case is presented in agricultural disease detecting area.

IRIS: A database application system for diseases identification using FTIR spectroscopy

NASA Astrophysics Data System (ADS)

Arshad, Ahmad Zulhilmi; Munajat, Yusof; Ibrahim, Raja Kamarulzaman Raja; Mahmood, Nasrul Humaimi

2015-05-01

Infrared information on diseases identification system (IRIS) is an application for diseases identification and analysis by using Fourier transform infrared (FTIR) spectroscopy. This is the preliminary step to gather information from the secondary data which was extracted from recognized various research and scientific paper, which are combined into a single database as in IRIS for our purpose of study. The importance of this database is to examine the fingerprint differences between normal and diseases cell or tissue. With the implementation of this application is it hopes that the diseases identification using FTIR spectroscopy would be more reliable and may assist either physicians, pathologists, or researchers to diagnose the certain type of disease efficiently.

Nonlinear dimensionality reduction methods for synthetic biology biobricks' visualization.

PubMed

Yang, Jiaoyun; Wang, Haipeng; Ding, Huitong; An, Ning; Alterovitz, Gil

2017-01-19

Visualizing data by dimensionality reduction is an important strategy in Bioinformatics, which could help to discover hidden data properties and detect data quality issues, e.g. data noise, inappropriately labeled data, etc. As crowdsourcing-based synthetic biology databases face similar data quality issues, we propose to visualize biobricks to tackle them. However, existing dimensionality reduction methods could not be directly applied on biobricks datasets. Hereby, we use normalized edit distance to enhance dimensionality reduction methods, including Isomap and Laplacian Eigenmaps. By extracting biobricks from synthetic biology database Registry of Standard Biological Parts, six combinations of various types of biobricks are tested. The visualization graphs illustrate discriminated biobricks and inappropriately labeled biobricks. Clustering algorithm K-means is adopted to quantify the reduction results. The average clustering accuracy for Isomap and Laplacian Eigenmaps are 0.857 and 0.844, respectively. Besides, Laplacian Eigenmaps is 5 times faster than Isomap, and its visualization graph is more concentrated to discriminate biobricks. By combining normalized edit distance with Isomap and Laplacian Eigenmaps, synthetic biology biobircks are successfully visualized in two dimensional space. Various types of biobricks could be discriminated and inappropriately labeled biobricks could be determined, which could help to assess crowdsourcing-based synthetic biology databases' quality, and make biobricks selection.

Characterizing rainfall in the Tenerife island

NASA Astrophysics Data System (ADS)

Díez-Sierra, Javier; del Jesus, Manuel; Losada Rodriguez, Inigo

2017-04-01

In many locations, rainfall data are collected through networks of meteorological stations. The data collection process is nowadays automated in many places, leading to the development of big databases of rainfall data covering extensive areas of territory. However, managers, decision makers and engineering consultants tend not to extract most of the information contained in these databases due to the lack of specific software tools for their exploitation. Here we present the modeling and development effort put in place in the Tenerife island in order to develop MENSEI-L, a software tool capable of automatically analyzing a complete rainfall database to simplify the extraction of information from observations. MENSEI-L makes use of weather type information derived from atmospheric conditions to separate the complete time series into homogeneous groups where statistical distributions are fitted. Normal and extreme regimes are obtained in this manner. MENSEI-L is also able to complete missing data in the time series and to generate synthetic stations by using Kriging techniques. These techniques also serve to generate the spatial regimes of precipitation, both normal and extreme ones. MENSEI-L makes use of weather type information to also provide a stochastic three-day probability forecast for rainfall.

A large scale analysis of cDNA in Arabidopsis thaliana: generation of 12,028 non-redundant expressed sequence tags from normalized and size-selected cDNA libraries.

PubMed

Asamizu, E; Nakamura, Y; Sato, S; Tabata, S

2000-06-30

For comprehensive analysis of genes expressed in the model dicotyledonous plant, Arabidopsis thaliana, expressed sequence tags (ESTs) were accumulated. Normalized and size-selected cDNA libraries were constructed from aboveground organs, flower buds, roots, green siliques and liquid-cultured seedlings, respectively, and a total of 14,026 5'-end ESTs and 39,207 3'-end ESTs were obtained. The 3'-end ESTs could be clustered into 12,028 non-redundant groups. Similarity search of the non-redundant ESTs against the public non-redundant protein database indicated that 4816 groups show similarity to genes of known function, 1864 to hypothetical genes, and the remaining 5348 are novel sequences. Gene coverage by the non-redundant ESTs was analyzed using the annotated genomic sequences of approximately 10 Mb on chromosomes 3 and 5. A total of 923 regions were hit by at least one EST, among which only 499 regions were hit by the ESTs deposited in the public database. The result indicates that the EST source generated in this project complements the EST data in the public database and facilitates new gene discovery.

Forensic odontology: A prosthodontic view

PubMed Central

Gosavi, Sulekha; Gosavi, Siddharth

2012-01-01

The most common role of the forensic dentist is the identification of deceased individuals. Dental identifications have always played a key role in natural and manmade disaster situations, and in particular, the mass casualties normally associated with aviation disasters. Because of the lack of a comprehensive fingerprint database, dental identification continues to be crucial in the world. An all-acrylic resin appliance such as a full denture or an all-acrylic partial denture (or orthodontic appliance), prior to delivery, could be inscribed with the patient's full name on a substrate (paper, metal) and sealed inconspicuously into the surface of a denture by various processes. It has been noted by several authors that in many cases of air disaster where the limbs are completely burnt off, some denture materials survive, especially the posterior part of acrylic dentures and metal-based dentures. Thus, marked dental prostheses (full and partial dentures, mouthguards and removal orthodontic appliances) would lead to rapid identification in the event of accidents and disaster. PMID:23087581

Keratoconus and Personality-A Review.

PubMed

Mannis, Mark J; Ling, Jennifer J; Kyrillos, Ralph; Barnett, Melissa

2018-03-01

To assess the existing literature on the subject of keratoconus and personality and to propose a theory that might account for the perceived personality changes associated with this condition. A literature search was conducted in the PubMed database using the term "keratoconus" in combination with keywords such as personality, psychiatry, psychology, anxiety, depression, or psychosis. A total of 15 articles pertaining to personality and psychiatric disorders in keratoconus were retained and reviewed. Although patients with keratoconus tend to score differently on personality scales compared with normal controls, the literature fails to substantiate the existence of a unique "keratoconic personality." Instead, patients with keratoconus prove to have more dysfunctional coping mechanisms that specifically alter their interaction with health care providers and may account for the persistent clinical impression of less respectful, conforming, and cooperative patients. We hypothesize that the stage of life at which keratoconus commonly presents plays a crucial role in personality and coping mechanism development that significantly affects behavioral patterns and the relationship with caregivers.

Bioconductor Workflow for Microbiome Data Analysis: from raw reads to community analyses

PubMed Central

Callahan, Ben J.; Sankaran, Kris; Fukuyama, Julia A.; McMurdie, Paul J.; Holmes, Susan P.

2016-01-01

High-throughput sequencing of PCR-amplified taxonomic markers (like the 16S rRNA gene) has enabled a new level of analysis of complex bacterial communities known as microbiomes. Many tools exist to quantify and compare abundance levels or OTU composition of communities in different conditions. The sequencing reads have to be denoised and assigned to the closest taxa from a reference database. Common approaches use a notion of 97% similarity and normalize the data by subsampling to equalize library sizes. In this paper, we show that statistical models allow more accurate abundance estimates. By providing a complete workflow in R, we enable the user to do sophisticated downstream statistical analyses, whether parametric or nonparametric. We provide examples of using the R packages dada2, phyloseq, DESeq2, ggplot2 and vegan to filter, visualize and test microbiome data. We also provide examples of supervised analyses using random forests and nonparametric testing using community networks and the ggnetwork package. PMID:27508062

Joint Feature Extraction and Classifier Design for ECG-Based Biometric Recognition.

PubMed

Gutta, Sandeep; Cheng, Qi

2016-03-01

Traditional biometric recognition systems often utilize physiological traits such as fingerprint, face, iris, etc. Recent years have seen a growing interest in electrocardiogram (ECG)-based biometric recognition techniques, especially in the field of clinical medicine. In existing ECG-based biometric recognition methods, feature extraction and classifier design are usually performed separately. In this paper, a multitask learning approach is proposed, in which feature extraction and classifier design are carried out simultaneously. Weights are assigned to the features within the kernel of each task. We decompose the matrix consisting of all the feature weights into sparse and low-rank components. The sparse component determines the features that are relevant to identify each individual, and the low-rank component determines the common feature subspace that is relevant to identify all the subjects. A fast optimization algorithm is developed, which requires only the first-order information. The performance of the proposed approach is demonstrated through experiments using the MIT-BIH Normal Sinus Rhythm database.

Automatic Mexican sign language and digits recognition using normalized central moments

NASA Astrophysics Data System (ADS)

Solís, Francisco; Martínez, David; Espinosa, Oscar; Toxqui, Carina

2016-09-01

This work presents a framework for automatic Mexican sign language and digits recognition based on computer vision system using normalized central moments and artificial neural networks. Images are captured by digital IP camera, four LED reflectors and a green background in order to reduce computational costs and prevent the use of special gloves. 42 normalized central moments are computed per frame and used in a Multi-Layer Perceptron to recognize each database. Four versions per sign and digit were used in training phase. 93% and 95% of recognition rates were achieved for Mexican sign language and digits respectively.

Understanding the health and social care needs of people living with IBD: A meta-synthesis of the evidence

PubMed Central

Kemp, Karen; Griffiths, Jane; Lovell, Karina

2012-01-01

AIM: To undertake a metasynthesis of qualitative studies to understand the health and social needs of people living with inflammatory bowel disease (IBD). METHODS: A systematic search strategy identified qualitative studies exploring the phenomenon of living with inflammatory bowel disease. Databases included MEDLINE, PsychInfo, EMBASE, CINAHL and the British Nursing Index via the OVID platform. Qualitative search filters were adapted from Hedges database (http://www.urmc.rochester.edu/hslt/miner/digital_library/tip_sheets/Cinahl_eb_filters.pdf). Qualitative empirical studies exploring the health and social needs of people living with inflammatory bowel disease were selected. Study eligibility and data extraction were independently completed using the Critical Appraisal Skills Programme for qualitative studies. The studies were analysed and synthesised using metasynthesis methodology. The themes from the studies allowed for common translations into a new interpretation of the impact of living with inflammatory bowel disease. RESULTS: Of 1395 studies, six published studies and one unpublished thesis fulfilled the inclusion criteria. First iteration of synthesis identified 16 themes, 2nd iteration synthesised these into three main 2nd order constructs: “detained by the disease”; “living in a world of disease” and “wrestling with life”. “Detained by the disease” is the fear of incontinence, the behaviour the patients display due to the fear, and the impact this has on the individual, such as social isolation and missing out on life events. All of these serve to “pull” the patient back from normal living. “Living in a world of disease” is the long term effects of living with a long term condition and the fear of these effects. “Wrestling with life” is the continued fight to thrive, the “push” to continue normal living. CONCLUSION: The metasynthesis provides a comprehensive representation of living with IBD. The unmistakeable burden of incontinence is exposed and its ongoing effects are demonstrated. The combined overall impact of living with IBD is the tension these patients live with: “Pushed and pulled: a compromised life”, people living with IBD experience a constant conflict throughout their lives, they push to be normal but IBD pulls them back. The impact of the fear of incontinence and behaviour of the individual as a result, requires further qualitative enquiry. PMID:23180944

A retrospective comparison of pregnancy outcomes between women with alpha-thalassaemia 1 trait and normal controls.

PubMed

Traisrisilp, Kuntharee; Jatavan, Phudit; Tongsong, Theera

2017-11-01

The objective of this retrospective cohort study was to compare pregnancy outcomes between low-risk pregnant women with alpha-thalassaemia-1 trait and normal controls. The database of the Maternal-Foetal Medicine unit was used to identify low-risk singleton pregnant women complicated by alpha-thalassaemia-1 trait who gave birth between January 2002 and October 2014. The low-risk pregnancies with non-carrier status for thalassaemia were assigned into the control group, with a control-to-case ratio of 10:1. During the study period, 595 women with alpha-thalassaemia-1 trait and 5950 normal controls were identified. There was no significant difference in the incidence of preterm birth and most obstetric outcomes between the two groups. However, a statistically significant difference was detected between them in terms of gestational age at delivery, 37.76 ± 2.81 vs. 38.11 ± 2.50 weeks (p = .001), birth weight, 2876 ± 581 vs. 2948 ± 527 g (p = .002) as well as the rate of low-birth weight, 17.1 vs. 12.8% (p = .002). In conclusion, this study provides new insights that alpha-thalassaemia-1 trait has minimal effect on gestational age at delivery and low-birth weight whereas other common adverse pregnancy outcomes are not increased. Impact statement What is already known on this subject: Thalassaemia trait is associated with some degree of anaemia. What the results of this study add: The prevalence of common adverse outcomes such as preterm birth, stillbirth, low Apgar scores and pregnancy-induced hypertension were not significantly different between both the groups, possibly caused by too small sample size to gain enough power. However, the rate of low-birth weight was significantly increased among pregnancy with alpha-thalassaemia-1 trait. What the implications are of these findings for clinical practice and/or further research: The information may be provided for alpha thalassaemia-1 trait mothers and their families. Physicians should guard against the occurrence of adverse pregnancy in these mothers. Prospective control study should be conducted to overcome the limitation of retrospective nature.

Nonparametric Bayesian Modeling for Automated Database Schema Matching

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

Ferragut, Erik M; Laska, Jason A

2015-01-01

The problem of merging databases arises in many government and commercial applications. Schema matching, a common first step, identifies equivalent fields between databases. We introduce a schema matching framework that builds nonparametric Bayesian models for each field and compares them by computing the probability that a single model could have generated both fields. Our experiments show that our method is more accurate and faster than the existing instance-based matching algorithms in part because of the use of nonparametric Bayesian models.

The influence of soil properties and nutrients on conifer forest growth in Sweden, and the first steps in developing a nutrient availability metric

NASA Astrophysics Data System (ADS)

Van Sundert, Kevin; Horemans, Joanna A.; Stendahl, Johan; Vicca, Sara

2018-06-01

The availability of nutrients is one of the factors that regulate terrestrial carbon cycling and modify ecosystem responses to environmental changes. Nonetheless, nutrient availability is often overlooked in climate-carbon cycle studies because it depends on the interplay of various soil factors that would ideally be comprised into metrics applicable at large spatial scales. Such metrics do not currently exist. Here, we use a Swedish forest inventory database that contains soil data and tree growth data for > 2500 forests across Sweden to (i) test which combination of soil factors best explains variation in tree growth, (ii) evaluate an existing metric of constraints on nutrient availability, and (iii) adjust this metric for boreal forest data. With (iii), we thus aimed to provide an adjustable nutrient metric, applicable for Sweden and with potential for elaboration to other regions. While taking into account confounding factors such as climate, N deposition, and soil oxygen availability, our analyses revealed that the soil organic carbon concentration (SOC) and the ratio of soil carbon to nitrogen (C : N) were the most important factors explaining variation in normalized (climate-independent) productivity (mean annual volume increment - m3 ha-1 yr-1) across Sweden. Normalized forest productivity was significantly negatively related to the soil C : N ratio (R2 = 0.02-0.13), while SOC exhibited an empirical optimum (R2 = 0.05-0.15). For the metric, we started from a (yet unvalidated) metric for constraints on nutrient availability that was previously developed by the International Institute for Applied Systems Analysis (IIASA - Laxenburg, Austria) for evaluating potential productivity of arable land. This IIASA metric requires information on soil properties that are indicative of nutrient availability (SOC, soil texture, total exchangeable bases - TEB, and pH) and is based on theoretical considerations that are also generally valid for nonagricultural ecosystems. However, the IIASA metric was unrelated to normalized forest productivity across Sweden (R2 = 0.00-0.01) because the soil factors under consideration were not optimally implemented according to the Swedish data, and because the soil C : N ratio was not included. Using two methods (each one based on a different way of normalizing productivity for climate), we adjusted this metric by incorporating soil C : N and modifying the relationship between SOC and nutrient availability in view of the observed relationships across our database. In contrast to the IIASA metric, the adjusted metrics explained some variation in normalized productivity in the database (R2 = 0.03-0.21; depending on the applied method). A test for five manually selected local fertility gradients in our database revealed a significant and stronger relationship between the adjusted metrics and productivity for each of the gradients (R2 = 0.09-0.38). This study thus shows for the first time how nutrient availability metrics can be evaluated and adjusted for a particular ecosystem type, using a large-scale database.

Time-critical Database Condition Data Handling in the CMS Experiment During the First Data Taking Period

NASA Astrophysics Data System (ADS)

Cavallari, Francesca; de Gruttola, Michele; Di Guida, Salvatore; Govi, Giacomo; Innocente, Vincenzo; Pfeiffer, Andreas; Pierro, Antonio

2011-12-01

Automatic, synchronous and reliable population of the condition databases is critical for the correct operation of the online selection as well as of the offline reconstruction and analysis of data. In this complex infrastructure, monitoring and fast detection of errors is a very challenging task. In this paper, we describe the CMS experiment system to process and populate the Condition Databases and make condition data promptly available both online for the high-level trigger and offline for reconstruction. The data are automatically collected using centralized jobs or are "dropped" by the users in dedicated services (offline and online drop-box), which synchronize them and take care of writing them into the online database. Then they are automatically streamed to the offline database, and thus are immediately accessible offline worldwide. The condition data are managed by different users using a wide range of applications.In normal operation the database monitor is used to provide simple timing information and the history of all transactions for all database accounts, and in the case of faults it is used to return simple error messages and more complete debugging information.

Drug-Path: a database for drug-induced pathways

PubMed Central

Zeng, Hui; Cui, Qinghua

2015-01-01

Some databases for drug-associated pathways have been built and are publicly available. However, the pathways curated in most of these databases are drug-action or drug-metabolism pathways. In recent years, high-throughput technologies such as microarray and RNA-sequencing have produced lots of drug-induced gene expression profiles. Interestingly, drug-induced gene expression profile frequently show distinct patterns, indicating that drugs normally induce the activation or repression of distinct pathways. Therefore, these pathways contribute to study the mechanisms of drugs and drug-repurposing. Here, we present Drug-Path, a database of drug-induced pathways, which was generated by KEGG pathway enrichment analysis for drug-induced upregulated genes and downregulated genes based on drug-induced gene expression datasets in Connectivity Map. Drug-Path provides user-friendly interfaces to retrieve, visualize and download the drug-induced pathway data in the database. In addition, the genes deregulated by a given drug are highlighted in the pathways. All data were organized using SQLite. The web site was implemented using Django, a Python web framework. Finally, we believe that this database will be useful for related researches. Database URL: http://www.cuilab.cn/drugpath PMID:26130661

Fullerene data mining using bibliometrics and database tomography

PubMed

Kostoff; Braun; Schubert; Toothman; Humenik

2000-01-01

Database tomography (DT) is a textual database analysis system consisting of two major components: (1) algorithms for extracting multiword phrase frequencies and phrase proximities (physical closeness of the multiword technical phrases) from any type of large textual database, to augment (2) interpretative capabilities of the expert human analyst. DT was used to derive technical intelligence from a fullerenes database derived from the Science Citation Index and the Engineering Compendex. Phrase frequency analysis by the technical domain experts provided the pervasive technical themes of the fullerenes database, and phrase proximity analysis provided the relationships among the pervasive technical themes. Bibliometric analysis of the fullerenes literature supplemented the DT results with author/journal/institution publication and citation data. Comparisons of fullerenes results with past analyses of similarly structured near-earth space, chemistry, hypersonic/supersonic flow, aircraft, and ship hydrodynamics databases are made. One important finding is that many of the normalized bibliometric distribution functions are extremely consistent across these diverse technical domains and could reasonably be expected to apply to broader chemical topics than fullerenes that span multiple structural classes. Finally, lessons learned about integrating the technical domain experts with the data mining tools are presented.

Data Publication and Interoperability for Long Tail Researchers via the Open Data Repository's (ODR) Data Publisher.

NASA Astrophysics Data System (ADS)

Stone, N.; Lafuente, B.; Bristow, T.; Keller, R.; Downs, R. T.; Blake, D. F.; Fonda, M.; Pires, A.

2016-12-01

Working primarily with astrobiology researchers at NASA Ames, the Open Data Repository (ODR) has been conducting a software pilot to meet the varying needs of this multidisciplinary community. Astrobiology researchers often have small communities or operate individually with unique data sets that don't easily fit into existing database structures. The ODR constructed its Data Publisher software to allow researchers to create databases with common metadata structures and subsequently extend them to meet their individual needs and data requirements. The software accomplishes these tasks through a web-based interface that allows collaborative creation and revision of common metadata templates and individual extensions to these templates for custom data sets. This allows researchers to search disparate datasets based on common metadata established through the metadata tools, but still facilitates distinct analyses and data that may be stored alongside the required common metadata. The software produces web pages that can be made publicly available at the researcher's discretion so that users may search and browse the data in an effort to make interoperability and data discovery a human-friendly task while also providing semantic data for machine-based discovery. Once relevant data has been identified, researchers can utilize the built-in application programming interface (API) that exposes the data for machine-based consumption and integration with existing data analysis tools (e.g. R, MATLAB, Project Jupyter - http://jupyter.org). The current evolution of the project has created the Astrobiology Habitable Environments Database (AHED)[1] which provides an interface to databases connected through a common metadata core. In the next project phase, the goal is for small research teams and groups to be self-sufficient in publishing their research data to meet funding mandates and academic requirements as well as fostering increased data discovery and interoperability through human-readable and machine-readable interfaces. This project is supported by the Science-Enabling Research Activity (SERA) and NASA NNX11AP82A, MSL. [1] B. Lafuente et al. (2016) AGU, submitted.

Nationwide Databases in Orthopaedic Surgery Research.

PubMed

Bohl, Daniel D; Singh, Kern; Grauer, Jonathan N

2016-10-01

The use of nationwide databases to conduct orthopaedic research has expanded markedly in recent years. Nationwide databases offer large sample sizes, sampling of patients who are representative of the country as a whole, and data that enable investigation of trends over time. The most common use of nationwide databases is to study the occurrence of postoperative adverse events. Other uses include the analysis of costs and the investigation of critical hospital metrics, such as length of stay and readmission rates. Although nationwide databases are powerful research tools, readers should be aware of the differences between them and their limitations. These include variations and potential inaccuracies in data collection, imperfections in patient sampling, insufficient postoperative follow-up, and lack of orthopaedic-specific outcomes.

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences.

PubMed

Stephens, Susie M; Chen, Jake Y; Davidson, Marcel G; Thomas, Shiby; Trute, Barry M

2005-01-01

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html.

Spatial database for a global assessment of undiscovered copper resources: Chapter Z in Global mineral resource assessment

USGS Publications Warehouse

Dicken, Connie L.; Dunlap, Pamela; Parks, Heather L.; Hammarstrom, Jane M.; Zientek, Michael L.; Zientek, Michael L.; Hammarstrom, Jane M.; Johnson, Kathleen M.

2016-07-13

As part of the first-ever U.S. Geological Survey global assessment of undiscovered copper resources, data common to several regional spatial databases published by the U.S. Geological Survey, including one report from Finland and one from Greenland, were standardized, updated, and compiled into a global copper resource database. This integrated collection of spatial databases provides location, geologic and mineral resource data, and source references for deposits, significant prospects, and areas permissive for undiscovered deposits of both porphyry copper and sediment-hosted copper. The copper resource database allows for efficient modeling on a global scale in a geographic information system (GIS) and is provided in an Esri ArcGIS file geodatabase format.

Common Postmortem Computed Tomography Findings Following Atraumatic Death: Differentiation between Normal Postmortem Changes and Pathologic Lesions

PubMed Central

Gonoi, Wataru; Okuma, Hidemi; Shirota, Go; Shintani, Yukako; Abe, Hiroyuki; Takazawa, Yutaka; Fukayama, Masashi; Ohtomo, Kuni

2015-01-01

Computed tomography (CT) is widely used in postmortem investigations as an adjunct to the traditional autopsy in forensic medicine. To date, several studies have described postmortem CT findings as being caused by normal postmortem changes. However, on interpretation, postmortem CT findings that are seemingly due to normal postmortem changes initially, may not have been mere postmortem artifacts. In this pictorial essay, we describe the common postmortem CT findings in cases of atraumatic in-hospital death and describe the diagnostic pitfalls of normal postmortem changes that can mimic real pathologic lesions. PMID:26175579

Supplier Management System

NASA Technical Reports Server (NTRS)

Ramirez, Eric; Gutheinz, Sandy; Brison, James; Ho, Anita; Allen, James; Ceritelli, Olga; Tobar, Claudia; Nguyen, Thuykien; Crenshaw, Harrel; Santos, Roxann

2008-01-01

Supplier Management System (SMS) allows for a consistent, agency-wide performance rating system for suppliers used by NASA. This version (2.0) combines separate databases into one central database that allows for the sharing of supplier data. Information extracted from the NBS/Oracle database can be used to generate ratings. Also, supplier ratings can now be generated in the areas of cost, product quality, delivery, and audit data. Supplier data can be charted based on real-time user input. Based on these individual ratings, an overall rating can be generated. Data that normally would be stored in multiple databases, each requiring its own log-in, is now readily available and easily accessible with only one log-in required. Additionally, the database can accommodate the storage and display of quality-related data that can be analyzed and used in the supplier procurement decision-making process. Moreover, the software allows for a Closed-Loop System (supplier feedback), as well as the capability to communicate with other federal agencies.

The EPIC nutrient database project (ENDB): a first attempt to standardize nutrient databases across the 10 European countries participating in the EPIC study.

PubMed

Slimani, N; Deharveng, G; Unwin, I; Southgate, D A T; Vignat, J; Skeie, G; Salvini, S; Parpinel, M; Møller, A; Ireland, J; Becker, W; Farran, A; Westenbrink, S; Vasilopoulou, E; Unwin, J; Borgejordet, A; Rohrmann, S; Church, S; Gnagnarella, P; Casagrande, C; van Bakel, M; Niravong, M; Boutron-Ruault, M C; Stripp, C; Tjønneland, A; Trichopoulou, A; Georga, K; Nilsson, S; Mattisson, I; Ray, J; Boeing, H; Ocké, M; Peeters, P H M; Jakszyn, P; Amiano, P; Engeset, D; Lund, E; de Magistris, M Santucci; Sacerdote, C; Welch, A; Bingham, S; Subar, A F; Riboli, E

2007-09-01

This paper describes the ad hoc methodological concepts and procedures developed to improve the comparability of Nutrient databases (NDBs) across the 10 European countries participating in the European Prospective Investigation into Cancer and Nutrition (EPIC). This was required because there is currently no European reference NDB available. A large network involving national compilers, nutritionists and experts on food chemistry and computer science was set up for the 'EPIC Nutrient DataBase' (ENDB) project. A total of 550-1500 foods derived from about 37,000 standardized EPIC 24-h dietary recalls (24-HDRS) were matched as closely as possible to foods available in the 10 national NDBs. The resulting national data sets (NDS) were then successively documented, standardized and evaluated according to common guidelines and using a DataBase Management System specifically designed for this project. The nutrient values of foods unavailable or not readily available in NDSs were approximated by recipe calculation, weighted averaging or adjustment for weight changes and vitamin/mineral losses, using common algorithms. The final ENDB contains about 550-1500 foods depending on the country and 26 common components. Each component value was documented and standardized for unit, mode of expression, definition and chemical method of analysis, as far as possible. Furthermore, the overall completeness of NDSs was improved (>or=99%), particularly for beta-carotene and vitamin E. The ENDB constitutes a first real attempt to improve the comparability of NDBs across European countries. This methodological work will provide a useful tool for nutritional research as well as end-user recommendations to improve NDBs in the future.

Demographic and epidemiologic characterization of transfusion recipients from four US regions: evidence from the REDS-III recipient database.

PubMed

Karafin, Matthew S; Bruhn, Roberta; Westlake, Matt; Sullivan, Marian T; Bialkowski, Walter; Edgren, Gustaf; Roubinian, Nareg H; Hauser, Ronald G; Kor, Daryl J; Fleischmann, Debra; Gottschall, Jerome L; Murphy, Edward L; Triulzi, Darrell J

2017-12-01

Blood transfusion is one of the most common medical procedures during hospitalization in the United States. To understand the benefits of transfusion while mitigating potential risks, a multicenter database containing detailed information on transfusion incidence and recipient outcomes would facilitate research. The Recipient Epidemiology and Donor Evaluation Study-III (REDS-III) program has developed a comprehensive transfusion recipient database utilizing data from hospital electronic health records at 12 participating hospitals in four geographic regions. Inpatient and outpatient data on transfusion recipients from January 1, 2013 to December 31, 2014 included patient age, sex, ethnicity, primary diagnosis, type of blood product provided, issue location, pretransfusion and post-transfusion hemoglobin (Hgb), and hospital outcomes. Transfusion incidence per encounter was calculated by blood product and various patient characteristics. During the 2-year study period, 80,362 (12.5%) inpatient encounters involved transfusion. Among inpatients, the most commonly transfused blood products were red blood cells (RBCs; 10.9% of encounters), followed by platelets (3.2%) and plasma (2.9%). Among patients who received transfusions, the median number of RBC units was one, the pretransfusion Hgb level was 7.6 g/dL, and the Hgb increment per unit was 1.4 g/dL. Encounter mortality increased with patient age, the number of units transfused, and the use of platelet or plasma products. The most commonly reported transfusion reaction was febrile nonhemolytic. The database contains comprehensive data regarding transfusion use and patient outcomes. The current report describes an evaluation of the first 2 years of a planned, 4-year, linked blood donor-component-recipient database, which represents a critical new resource for transfusion medicine researchers. © 2017 AABB.

Generation of comprehensive thoracic oncology database--tool for translational research.

PubMed

Surati, Mosmi; Robinson, Matthew; Nandi, Suvobroto; Faoro, Leonardo; Demchuk, Carley; Kanteti, Rajani; Ferguson, Benjamin; Gangadhar, Tara; Hensing, Thomas; Hasina, Rifat; Husain, Aliya; Ferguson, Mark; Karrison, Theodore; Salgia, Ravi

2011-01-22

The Thoracic Oncology Program Database Project was created to serve as a comprehensive, verified, and accessible repository for well-annotated cancer specimens and clinical data to be available to researchers within the Thoracic Oncology Research Program. This database also captures a large volume of genomic and proteomic data obtained from various tumor tissue studies. A team of clinical and basic science researchers, a biostatistician, and a bioinformatics expert was convened to design the database. Variables of interest were clearly defined and their descriptions were written within a standard operating manual to ensure consistency of data annotation. Using a protocol for prospective tissue banking and another protocol for retrospective banking, tumor and normal tissue samples from patients consented to these protocols were collected. Clinical information such as demographics, cancer characterization, and treatment plans for these patients were abstracted and entered into an Access database. Proteomic and genomic data have been included in the database and have been linked to clinical information for patients described within the database. The data from each table were linked using the relationships function in Microsoft Access to allow the database manager to connect clinical and laboratory information during a query. The queried data can then be exported for statistical analysis and hypothesis generation.

A database paradigm for the management of DICOM-RT structure sets using a geographic information system

NASA Astrophysics Data System (ADS)

Shao, Weber; Kupelian, Patrick A.; Wang, Jason; Low, Daniel A.; Ruan, Dan

2014-03-01

We devise a paradigm for representing the DICOM-RT structure sets in a database management system, in such way that secondary calculations of geometric information can be performed quickly from the existing contour definitions. The implementation of this paradigm is achieved using the PostgreSQL database system and the PostGIS extension, a geographic information system commonly used for encoding geographical map data. The proposed paradigm eliminates the overhead of retrieving large data records from the database, as well as the need to implement various numerical and data parsing routines, when additional information related to the geometry of the anatomy is desired.

Using the TIGR gene index databases for biological discovery.

PubMed

Lee, Yuandan; Quackenbush, John

2003-11-01

The TIGR Gene Index web pages provide access to analyses of ESTs and gene sequences for nearly 60 species, as well as a number of resources derived from these. Each species-specific database is presented using a common format with a homepage. A variety of methods exist that allow users to search each species-specific database. Methods implemented currently include nucleotide or protein sequence queries using WU-BLAST, text-based searches using various sequence identifiers, searches by gene, tissue and library name, and searches using functional classes through Gene Ontology assignments. This protocol provides guidance for using the Gene Index Databases to extract information.

The validity of arterial measurements in a South African embalmed body population.

PubMed

Schoeman, Marelize; van Schoor, Albert; Suleman, Farhana; Louw, Liebie; du Toit, Peet

2018-01-01

Knowledge of the normal arterial diameter at a given anatomical point is the first step toward quantifying the severity of cardiovascular diseases. According to several studies, parameters such as weight, height, age and sex can explain morphometric variations in arterial anatomy that are observed in a population. Before the development of a reference database against which to compare the diameters of arteries in a variety of pathological conditions, the compatibility between embalmed body measurements and computed tomography (CT) measurements must first be established. The aim of this study was to compare embalmed body measurements and CT measurements at 19 different arterial sites to establish whether embalmed body measurements are a true reflection of a living population. A total of 154 embalmed bodies were randomly selected from the Department of Anatomy at the University of Pretoria and 36 embalmed bodies were randomly selected from the Department of Human Anatomy at the University of Limpopo, Medunsa Campus. Dissections were performed on the embalmed body sample and the arterial dimensions were measured with a mechanical dial-sliding caliper (accuracy of 0.01 mm). 30 CT images for each of the 19 arterial sites were retrospectively selected from the database of radiographic images at the Department of Radiology, Steve Biko Academic Hospital. Radiant, a Digital Imaging and Communications in Medicine (DICOM) viewer was used to analyze the CT images. The only statistically significant differences between the embalmed body measurements and CT measurements were found in the left common carotid- and the left subclavian arteries. The null hypothesis of no statistically significant difference between the embalmed body and CT measurements was accepted since the P value indicated no significant difference for 87% of the measurements, the exception being the left common carotid- and the left subclavian arteries. With the exception of two measurements, measurements in embalmed bodies and living people are interchangeable and concerns regarding the effect of distortion and shrinkage are unfounded. Even small changes in arterial diameter greatly influence blood flow and blood pressure, which contribute to undesirable clinical outcomes such as aortic aneurysms and aortic dissections. This study completes the first step towards the development of a reference database against which to compare the diameters of arteries in a variety of pathological conditions in a South African population.

Genic insights from integrated human proteomics in GeneCards.

PubMed

Fishilevich, Simon; Zimmerman, Shahar; Kohn, Asher; Iny Stein, Tsippi; Olender, Tsviya; Kolker, Eugene; Safran, Marilyn; Lancet, Doron

2016-01-01

GeneCards is a one-stop shop for searchable human gene annotations (http://www.genecards.org/). Data are automatically mined from ∼120 sources and presented in an integrated web card for every human gene. We report the application of recent advances in proteomics to enhance gene annotation and classification in GeneCards. First, we constructed the Human Integrated Protein Expression Database (HIPED), a unified database of protein abundance in human tissues, based on the publically available mass spectrometry (MS)-based proteomics sources ProteomicsDB, Multi-Omics Profiling Expression Database, Protein Abundance Across Organisms and The MaxQuant DataBase. The integrated database, residing within GeneCards, compares favourably with its individual sources, covering nearly 90% of human protein-coding genes. For gene annotation and comparisons, we first defined a protein expression vector for each gene, based on normalized abundances in 69 normal human tissues. This vector is portrayed in the GeneCards expression section as a bar graph, allowing visual inspection and comparison. These data are juxtaposed with transcriptome bar graphs. Using the protein expression vectors, we further defined a pairwise metric that helps assess expression-based pairwise proximity. This new metric for finding functional partners complements eight others, including sharing of pathways, gene ontology (GO) terms and domains, implemented in the GeneCards Suite. In parallel, we calculated proteome-based differential expression, highlighting a subset of tissues that overexpress a gene and subserving gene classification. This textual annotation allows users of VarElect, the suite's next-generation phenotyper, to more effectively discover causative disease variants. Finally, we define the protein-RNA expression ratio and correlation as yet another attribute of every gene in each tissue, adding further annotative information. The results constitute a significant enhancement of several GeneCards sections and help promote and organize the genome-wide structural and functional knowledge of the human proteome. Database URL:http://www.genecards.org/. © The Author(s) 2016. Published by Oxford University Press.

Association of renal function and symptoms with mortality in star fruit (Averrhoa carambola) intoxication.

PubMed

Chua, Choon-Bing; Sun, Cheuk-Kwan; Tsui, Huan-Wen; Yang, Po-Jen; Lee, Kuo-Hsin; Hsu, Chih-Wei; Tsai, I-Ting

2017-08-01

Star fruit (SF) is a commonly available fruit produced and eaten in tropical and subtropical countries. Since 1993, various reports have described neurotoxicity after eating SF, but this clinical condition remains unfamiliar. We aimed to describe this clinical entity, the role of renal dysfunction in this disorder, treatment strategies, and prognosis of patients with SF intoxication. We conducted a search of PubMed and Google Scholar databases from 1993 to 2016. We included reports describing patients with a clear history of SF ingestion with acute symptoms. We described the demographic characteristics, reported SF intake, treatments used, and outcomes. We reviewed totally 126 patients (male:female = 1.5:1) from 33 articles with mean age 54.4 ± 11 (range: 30-84). The most common symptom was hiccups (65%), whereas confusion and seizure were the most common symptoms associated with mortality (42% and 61%, respectively). Pre-intoxication renal function also affected mortality. While there was no mortality in patients with normal renal function (NRF), the mortality of patients among reported cases with chronic renal insufficiency and end-stage renal disease undergoing dialysis were 36% and 27%, respectively. With the inclusion of patients reported to have NRF, the overall mortality was 24%. Consistently, the number of SF consumed was substantially higher in the patients with NRF than those with renal functional impairment. The most common treatment strategy was hemodialysis (59%). Patients with impaired renal function were at higher risks of SF intoxication. Severe neurologic symptoms mandate immediate medical intervention because of the association between their occurrence and high mortalities. Toxin removal through dialysis, rather than symptomatic relief, seems to be beneficial to patient survival. Early and continuous dialysis appears to alleviate severe symptoms and prevent symptom rebounds.

Murine fetal echocardiography.

PubMed

Kim, Gene H

2013-02-15

Transgenic mice displaying abnormalities in cardiac development and function represent a powerful tool for the understanding the molecular mechanisms underlying both normal cardiovascular function and the pathophysiological basis of human cardiovascular disease. Fetal and perinatal death is a common feature when studying genetic alterations affecting cardiac development. In order to study the role of genetic or pharmacologic alterations in the early development of cardiac function, ultrasound imaging of the live fetus has become an important tool for early recognition of abnormalities and longitudinal follow-up. Noninvasive ultrasound imaging is an ideal method for detecting and studying congenital malformations and the impact on cardiac function prior to death. It allows early recognition of abnormalities in the living fetus and the progression of disease can be followed in utero with longitudinal studies. Until recently, imaging of fetal mouse hearts frequently involved invasive methods. The fetus had to be sacrificed to perform magnetic resonance microscopy and electron microscopy or surgically delivered for transillumination microscopy. An application of high-frequency probes with conventional 2-D and pulsed-wave Doppler imaging has been shown to provide measurements of cardiac contraction and heart rates during embryonic development with databases of normal developmental changes now available. M-mode imaging further provides important functional data, although, the proper imaging planes are often difficult to obtain. High-frequency ultrasound imaging of the fetus has improved 2-D resolution and can provide excellent information on the early development of cardiac structures.

An updated concept of coagulation with clinical implications.

PubMed

Romney, Gregory; Glick, Michael

2009-05-01

Over the past century, a series of models have been put forth to explain the coagulation mechanism. The coagulation cascade/waterfall model has gained the most widespread acceptance. This model, however, has problems when it is used in different clinical scenarios. A more recently proposed cell-based model better describes the coagulation process in vivo and provides oral health care professionals (OHCPs) with a better understanding of the clinical implications of providing dental care to patients with potentially increased bleeding tendencies. The authors conducted a literature search using the PubMed database. They searched for key words including "coagulation," "hemostasis," "bleeding," "coagulation factors," "models," "prothrombin time," "activated partial thromboplastin time," "international normalized ratio," "anticoagulation therapy" and "hemophilia" separately and in combination. The coagulation cascade/waterfall model is insufficient to explain coagulation in vivo, predict a patient's bleeding tendency, or correlate clinical outcomes with specific laboratory screening tests such as prothrombin time, activated partial thromboplastin time and international normalized ratio. However, the cell-based model of coagulation that reflects the in vivo process of coagulation provides insight into the clinical ramifications of treating dental patients with specific coagulation factor deficiencies. Understanding the in vivo coagulation process will help OHCPs better predict a patient's bleeding tendency. In addition, applying the theoretical concept of the cell-based model of coagulation to commonly used laboratory screening tests for coagulation and bleeding will result in safer and more appropriate dental care.

Carbohydrates for improving the cognitive performance of independent-living older adults with normal cognition or mild cognitive impairment.

PubMed

Ooi, Cheow Peng; Loke, Seng Cheong; Yassin, Zaitun; Hamid, Tengku-Aizan

2011-04-13

Mild cognitive impairment (MCI) is an intermediate state between normal cognition and dementia in which daily function is largely intact. This condition may present an opportunity for research into the prevention of dementia. Carbohydrate is an essential and easily accessible macronutrient which influences cognitive performance. A better understanding of carbohydrate-driven cognitive changes in normal cognition and mild cognitive impairment may suggest ways to prevent or reduce cognitive decline. To assess the effectiveness of carbohydrates in improving cognitive function in older adults. We searched ALOIS, the Cochrane Dementia and Cognitive Improvement Group Specialized Register on 22 June 2010 using the terms: carbohydrates OR carbohydrate OR monosaccharides OR disaccharides OR oligosaccharides OR polysaccharides OR CARBS. ALOIS contains records from all major healthcare databases (The Cochrane Library, MEDLINE, EMBASE, PsycINFO, CINAHL, LILACS) as well as from many trial databases and grey literature sources. All randomised controlled trials (RCT) that have examined the efficacy of any form of carbohydrates in normal cognition and MCI. One review author selected and retrieved relevant articles for further assessment. The remaining authors independently assessed whether any of the retrieved trials should be included. Disagreements were resolved by discussion.  There is no suitable RCT of any form of carbohydrates involving independent-living older adults with normal cognition or mild cognitive impairment. There are no suitable RCTs on which to base any recommendations about the use of any form of carbohydrate for enhancing cognitive performance in older adults with normal cognition or mild cognitive impairment. More studies of many different carbohydrates are needed to tease out complex nutritional issues and further evaluate memory improvement.

Exudate detection in color retinal images for mass screening of diabetic retinopathy.

PubMed

Zhang, Xiwei; Thibault, Guillaume; Decencière, Etienne; Marcotegui, Beatriz; Laÿ, Bruno; Danno, Ronan; Cazuguel, Guy; Quellec, Gwénolé; Lamard, Mathieu; Massin, Pascale; Chabouis, Agnès; Victor, Zeynep; Erginay, Ali

2014-10-01

The automatic detection of exudates in color eye fundus images is an important task in applications such as diabetic retinopathy screening. The presented work has been undertaken in the framework of the TeleOphta project, whose main objective is to automatically detect normal exams in a tele-ophthalmology network, thus reducing the burden on the readers. A new clinical database, e-ophtha EX, containing precisely manually contoured exudates, is introduced. As opposed to previously available databases, e-ophtha EX is very heterogeneous. It contains images gathered within the OPHDIAT telemedicine network for diabetic retinopathy screening. Image definition, quality, as well as patients condition or the retinograph used for the acquisition, for example, are subject to important changes between different examinations. The proposed exudate detection method has been designed for this complex situation. We propose new preprocessing methods, which perform not only normalization and denoising tasks, but also detect reflections and artifacts in the image. A new candidates segmentation method, based on mathematical morphology, is proposed. These candidates are characterized using classical features, but also novel contextual features. Finally, a random forest algorithm is used to detect the exudates among the candidates. The method has been validated on the e-ophtha EX database, obtaining an AUC of 0.95. It has been also validated on other databases, obtaining an AUC between 0.93 and 0.95, outperforming state-of-the-art methods. Copyright © 2014 Elsevier B.V. All rights reserved.

Digital hand atlas for web-based bone age assessment: system design and implementation

NASA Astrophysics Data System (ADS)

Cao, Fei; Huang, H. K.; Pietka, Ewa; Gilsanz, Vicente

2000-04-01

A frequently used assessment method of skeletal age is atlas matching by a radiological examination of a hand image against a small set of Greulich-Pyle patterns of normal standards. The method however can lead to significant deviation in age assessment, due to a variety of observers with different levels of training. The Greulich-Pyle atlas based on middle upper class white populations in the 1950s, is also not fully applicable for children of today, especially regarding the standard development in other racial groups. In this paper, we present our system design and initial implementation of a digital hand atlas and computer-aided diagnostic (CAD) system for Web-based bone age assessment. The digital atlas will remove the disadvantages of the currently out-of-date one and allow the bone age assessment to be computerized and done conveniently via Web. The system consists of a hand atlas database, a CAD module and a Java-based Web user interface. The atlas database is based on a large set of clinically normal hand images of diverse ethnic groups. The Java-based Web user interface allows users to interact with the hand image database form browsers. Users can use a Web browser to push a clinical hand image to the CAD server for a bone age assessment. Quantitative features on the examined image, which reflect the skeletal maturity, is then extracted and compared with patterns from the atlas database to assess the bone age.

Validation of a common data model for active safety surveillance research

PubMed Central

Ryan, Patrick B; Reich, Christian G; Hartzema, Abraham G; Stang, Paul E

2011-01-01

Objective Systematic analysis of observational medical databases for active safety surveillance is hindered by the variation in data models and coding systems. Data analysts often find robust clinical data models difficult to understand and ill suited to support their analytic approaches. Further, some models do not facilitate the computations required for systematic analysis across many interventions and outcomes for large datasets. Translating the data from these idiosyncratic data models to a common data model (CDM) could facilitate both the analysts' understanding and the suitability for large-scale systematic analysis. In addition to facilitating analysis, a suitable CDM has to faithfully represent the source observational database. Before beginning to use the Observational Medical Outcomes Partnership (OMOP) CDM and a related dictionary of standardized terminologies for a study of large-scale systematic active safety surveillance, the authors validated the model's suitability for this use by example. Validation by example To validate the OMOP CDM, the model was instantiated into a relational database, data from 10 different observational healthcare databases were loaded into separate instances, a comprehensive array of analytic methods that operate on the data model was created, and these methods were executed against the databases to measure performance. Conclusion There was acceptable representation of the data from 10 observational databases in the OMOP CDM using the standardized terminologies selected, and a range of analytic methods was developed and executed with sufficient performance to be useful for active safety surveillance. PMID:22037893

Intelligent printing system with AMPAC: boot program for printing machine with AMPAC

NASA Astrophysics Data System (ADS)

Yuasa, Tomonori; Mishina, Hiromichi

2000-12-01

The database AMPAC proposes the simple and unified format to describe single parameter of whole field of design, production and management. The database described by the format can be used commonly in any field connected by the network production system, since the description accepts any parameter in any fields and is field independent definition.

Drug-Associated Acute Kidney Injury Identified in the United States Food and Drug Administration Adverse Event Reporting System Database.

PubMed

Welch, Hanna K; Kellum, John A; Kane-Gill, Sandra L

2018-06-08

Acute kidney injury (AKI) is a common condition associated with both short-term and long-term consequences including dialysis, chronic kidney disease, and mortality. Although the United States Food and Drug Administration Adverse Event Reporting System (FAERS) database is a powerful tool to examine drug-associated events, to our knowledge, no study has analyzed this database to identify the most common drugs reported with AKI. The objective of this study was to analyze AKI reports and associated medications in the FAERS database. Retrospective pharmacovigilance disproportionality analysis. FAERS database. We queried the FAERS database for reports of AKI from 2004 quarter 1 through 2015 quarter 3. Extracted drugs were assessed using published references and categorized as known, possible, or new potential nephrotoxins. The reporting odds ratio (ROR), a measure of reporting disproportionality, was calculated for the 20 most frequently reported drugs in each category. We retrieved 7,241,385 adverse event reports, of which 193,996 (2.7%) included a report of AKI. Of the AKI reports, 16.5% were known nephrotoxins, 18.6% were possible nephrotoxins, and 64.8% were new potential nephrotoxins. Among the most commonly reported drugs, those with the highest AKI ROR were aprotinin (7,614 reports; ROR 115.70, 95% confidence interval [CI] 110.63-121.01), sodium phosphate (1,687 reports; ROR 55.81, 95% CI 51.78-60.17), furosemide (1,743 reports; ROR 12.61, 95% CI 11.94-13.32), vancomycin (1,270 reports, ROR 12.19, 95% CI 11.45-12.99), and metformin (4,701 reports; ROR 10.65, 95% CI 10.31-11.00). The combined RORs for the 20 most frequently reported drugs with each nephrotoxin classification were 3.71 (95% CI 3.66-3.76) for known nephrotoxins, 2.09 (95% CI 2.06-2.12) for possible nephrotoxins, and 1.55 (95% CI 1.53-1.57) for new potential nephrotoxins. AKI was a common reason for adverse event reporting in the FAERS. Most AKI reports were generated for medications not recognized as nephrotoxic according to our classification system. This report provides data on medications needing further research to determine the risk of AKI with these new potential nephrotoxins. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Identifying common donors in DNA mixtures, with applications to database searches.

PubMed

Slooten, K

2017-01-01

Several methods exist to compute the likelihood ratio LR(M, g) evaluating the possible contribution of a person of interest with genotype g to a mixed trace M. In this paper we generalize this LR to a likelihood ratio LR(M 1 , M 2 ) involving two possibly mixed traces M 1 and M 2 , where the question is whether there is a donor in common to both traces. In case one of the traces is in fact a single genotype, then this likelihood ratio reduces to the usual LR(M, g). We explain how our method conceptually is a logical consequence of the fact that LR calculations of the form LR(M, g) can be equivalently regarded as a probabilistic deconvolution of the mixture. Based on simulated data, and using a semi-continuous mixture evaluation model, we derive ROC curves of our method applied to various types of mixtures. From these data we conclude that searches for a common donor are often feasible in the sense that a very small false positive rate can be combined with a high probability to detect a common donor if there is one. We also show how database searches comparing all traces to each other can be carried out efficiently, as illustrated by the application of the method to the mixed traces in the Dutch DNA database. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

SPSmart: adapting population based SNP genotype databases for fast and comprehensive web access.

PubMed

Amigo, Jorge; Salas, Antonio; Phillips, Christopher; Carracedo, Angel

2008-10-10

In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of human diversity, and are widely used as reference sources for population genetics studies. Although many useful conclusions may be extracted by querying databases individually, the lack of flexibility for combining data from within and between each database does not allow the calculation of key population variability statistics. We have developed a novel tool for accessing and combining large-scale genomic databases of single nucleotide polymorphisms (SNPs) in widespread use in human population genetics: SPSmart (SNPs for Population Studies). A fast pipeline creates and maintains a data mart from the most commonly accessed databases of genotypes containing population information: data is mined, summarized into the standard statistical reference indices, and stored into a relational database that currently handles as many as 4 x 10(9) genotypes and that can be easily extended to new database initiatives. We have also built a web interface to the data mart that allows the browsing of underlying data indexed by population and the combining of populations, allowing intuitive and straightforward comparison of population groups. All the information served is optimized for web display, and most of the computations are already pre-processed in the data mart to speed up the data browsing and any computational treatment requested. In practice, SPSmart allows populations to be combined into user-defined groups, while multiple databases can be accessed and compared in a few simple steps from a single query. It performs the queries rapidly and gives straightforward graphical summaries of SNP population variability through visual inspection of allele frequencies outlined in standard pie-chart format. In addition, full numerical description of the data is output in statistical results panels that include common population genetics metrics such as heterozygosity, Fst and In.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases.

PubMed

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-10-18

Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at http://www.ebi.ac.uk/Tools/picr.

The Protein Identifier Cross-Referencing (PICR) service: reconciling protein identifiers across multiple source databases

PubMed Central

Côté, Richard G; Jones, Philip; Martens, Lennart; Kerrien, Samuel; Reisinger, Florian; Lin, Quan; Leinonen, Rasko; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another. Partial solutions for protein identifier mapping exist but they are limited to specific species or techniques and to a very small number of databases. As a result, we have not found a solution that is generic enough and broad enough in mapping scope to suit our needs. Results We have created the Protein Identifier Cross-Reference (PICR) service, a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references based on 100% sequence identity to proteins from over 70 distinct source databases loaded into UniParc. Mappings can be limited by source database, taxonomic ID and activity status in the source database. Users can copy/paste or upload files containing protein identifiers or sequences in FASTA format to obtain mappings using the interactive interface. Search results can be viewed in simple or detailed HTML tables or downloaded as comma-separated values (CSV) or Microsoft Excel (XLS) files suitable for use in a local database or a spreadsheet. Alternatively, a SOAP interface is available to integrate PICR functionality in other applications, as is a lightweight REST interface. Conclusion We offer a publicly available service that can interactively map protein identifiers and protein sequences to the majority of commonly used protein databases. Programmatic access is available through a standards-compliant SOAP interface or a lightweight REST interface. The PICR interface, documentation and code examples are available at . PMID:17945017

Investigation on Chinese herbal medicine for primary dysmenorrhea: implication from a nationwide prescription database in Taiwan.

PubMed

Chen, Hsing-Yu; Lin, Yi-Hsuan; Su, Irene H; Chen, Yu-Chun; Yang, Sien-Hung; Chen, Jiun-Liang

2014-02-01

Primary dysmenorrhea is a common gynecological condition, for which Chinese herbal medicine (CHM) has been widely used in addition to western medicine. The aim of this study is to explore CHM commonly used to treat dysmenorrhea in young Chinese women. Observational retrospective study. The National Health Insurance Research Database in Taiwan. Women aged from 13 to 25 years with single diagnosis of primary dysmenorrhea. CHM prescriptions made for primary dysmenorrhea women during 1998-2008 were extracted to build up CHM prescription database. Association rule mining was used to explore the prevalent CHM combination patterns in treating primary dysmenorrhea. Prevalence and mechanisms of CHM combinations. Totally 57,315 prescriptions were analyzed and, on average, 5.3 CHM was used in one prescription. Dang-Gui-Shao-Yao-San (DGSYS) was the most commonly used herbal formula (27.2%), followed by Jia-Wei-Xiao-Yao-San (JWXYS) (20.7%) and Wen-Jing-Tang (WJT) (20.5%). Corydalis yanhusuo and Cyperus rotundus were the most commonly used single herb, found in 33.1% and 29.2% of all prescriptions. Additionally, C. yanhusuo with C. rotundus is the most commonly used two CHM in combination, accounting for 14.24% of all prescriptions, followed by DGSYS with C. yanhusuo (10.47%). Multi-target effects on primary dysmenorrhea, such as analgesia, mood modifying and hormone adjustment, were found among commonly prescribed CHM in this study. This study discovered the potential importance of C. yanhusuo, C. rotundus and DGSYS in treating primary dysmenorrhea. Further clinical trials or bench studies are warranted based on the results. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Using Web Ontology Language to Integrate Heterogeneous Databases in the Neurosciences

PubMed Central

Lam, Hugo Y.K.; Marenco, Luis; Shepherd, Gordon M.; Miller, Perry L.; Cheung, Kei-Hoi

2006-01-01

Integrative neuroscience involves the integration and analysis of diverse types of neuroscience data involving many different experimental techniques. This data will increasingly be distributed across many heterogeneous databases that are web-accessible. Currently, these databases do not expose their schemas (database structures) and their contents to web applications/agents in a standardized, machine-friendly way. This limits database interoperation. To address this problem, we describe a pilot project that illustrates how neuroscience databases can be expressed using the Web Ontology Language, which is a semantically-rich ontological language, as a common data representation language to facilitate complex cross-database queries. In this pilot project, an existing tool called “D2RQ” was used to translate two neuroscience databases (NeuronDB and CoCoDat) into OWL, and the resulting OWL ontologies were then merged. An OWL-based reasoner (Racer) was then used to provide a sophisticated query language (nRQL) to perform integrated queries across the two databases based on the merged ontology. This pilot project is one step toward exploring the use of semantic web technologies in the neurosciences. PMID:17238384

Statistical properties of the normalized ice particle size distribution

NASA Astrophysics Data System (ADS)

Delanoë, Julien; Protat, Alain; Testud, Jacques; Bouniol, Dominique; Heymsfield, A. J.; Bansemer, A.; Brown, P. R. A.; Forbes, R. M.

2005-05-01

Testud et al. (2001) have recently developed a formalism, known as the "normalized particle size distribution (PSD)", which consists in scaling the diameter and concentration axes in such a way that the normalized PSDs are independent of water content and mean volume-weighted diameter. In this paper we investigate the statistical properties of the normalized PSD for the particular case of ice clouds, which are known to play a crucial role in the Earth's radiation balance. To do so, an extensive database of airborne in situ microphysical measurements has been constructed. A remarkable stability in shape of the normalized PSD is obtained. The impact of using a single analytical shape to represent all PSDs in the database is estimated through an error analysis on the instrumental (radar reflectivity and attenuation) and cloud (ice water content, effective radius, terminal fall velocity of ice crystals, visible extinction) properties. This resulted in a roughly unbiased estimate of the instrumental and cloud parameters, with small standard deviations ranging from 5 to 12%. This error is found to be roughly independent of the temperature range. This stability in shape and its single analytical approximation implies that two parameters are now sufficient to describe any normalized PSD in ice clouds: the intercept parameter N*0 and the mean volume-weighted diameter Dm. Statistical relationships (parameterizations) between N*0 and Dm have then been evaluated in order to reduce again the number of unknowns. It has been shown that a parameterization of N*0 and Dm by temperature could not be envisaged to retrieve the cloud parameters. Nevertheless, Dm-T and mean maximum dimension diameter -T parameterizations have been derived and compared to the parameterization of Kristjánsson et al. (2000) currently used to characterize particle size in climate models. The new parameterization generally produces larger particle sizes at any temperature than the Kristjánsson et al. (2000) parameterization. These new parameterizations are believed to better represent particle size at global scale, owing to a better representativity of the in situ microphysical database used to derive it. We then evaluated the potential of a direct N*0-Dm relationship. While the model parameterized by temperature produces strong errors on the cloud parameters, the N*0-Dm model parameterized by radar reflectivity produces accurate cloud parameters (less than 3% bias and 16% standard deviation). This result implies that the cloud parameters can be estimated from the estimate of only one parameter of the normalized PSD (N*0 or Dm) and a radar reflectivity measurement.

Classification of cardiac rhythm using heart rate dynamical measures: validation in MIT-BIH databases.

PubMed

Carrara, Marta; Carozzi, Luca; Moss, Travis J; de Pasquale, Marco; Cerutti, Sergio; Lake, Douglas E; Moorman, J Randall; Ferrario, Manuela

2015-01-01

Identification of atrial fibrillation (AF) is a clinical imperative. Heartbeat interval time series are increasingly available from personal monitors, allowing new opportunity for AF diagnosis. Previously, we devised numerical algorithms for identification of normal sinus rhythm (NSR), AF, and SR with frequent ectopy using dynamical measures of heart rate. Here, we wished to validate them in the canonical MIT-BIH ECG databases. We tested algorithms on the NSR, AF and arrhythmia databases. When the databases were combined, the positive predictive value of the new algorithms exceeded 95% for NSR and AF, and was 40% for SR with ectopy. Further, dynamical measures did not distinguish atrial from ventricular ectopy. Inspection of individual 24hour records showed good correlation of observed and predicted rhythms. Heart rate dynamical measures are effective ingredients in numerical algorithms to classify cardiac rhythm from the heartbeat intervals time series alone. Copyright © 2015 Elsevier Inc. All rights reserved.

Database of episode-integrated solar energetic proton fluences

NASA Astrophysics Data System (ADS)

Robinson, Zachary D.; Adams, James H.; Xapsos, Michael A.; Stauffer, Craig A.

2018-04-01

A new database of proton episode-integrated fluences is described. This database contains data from two different instruments on multiple satellites. The data are from instruments on the Interplanetary Monitoring Platform-8 (IMP8) and the Geostationary Operational Environmental Satellites (GOES) series. A method to normalize one set of data to one another is presented to create a seamless database spanning 1973 to 2016. A discussion of some of the characteristics that episodes exhibit is presented, including episode duration and number of peaks. As an example of what can be understood about episodes, the July 4, 2012 episode is examined in detail. The coronal mass ejections and solar flares that caused many of the fluctuations of the proton flux seen at Earth are associated with peaks in the proton flux during this episode. The reasoning for each choice is laid out to provide a reference for how CME and solar flares associations are made.

Transcriptome analysis of duck liver and identification of differentially expressed transcripts in response to duck hepatitis A virus genotype C infection.

PubMed

Tang, Cheng; Lan, Daoliang; Zhang, Huanrong; Ma, Jing; Yue, Hua

2013-01-01

Duck is an economically important poultry and animal model for human viral hepatitis B. However, the molecular mechanisms underlying host-virus interaction remain unclear because of limited information on the duck genome. This study aims to characterize the duck normal liver transcriptome and to identify the differentially expressed transcripts at 24 h after duck hepatitis A virus genotype C (DHAV-C) infection using Illumina-Solexa sequencing. After removal of low-quality sequences and assembly, a total of 52,757 unigenes was obtained from the normal liver group. Further blast analysis showed that 18,918 unigenes successfully matched the known genes in the database. GO analysis revealed that 25,116 unigenes took part in 61 categories of biological processes, cellular components, and molecular functions. Among the 25 clusters of orthologous group categories (COG), the cluster for "General function prediction only" represented the largest group, followed by "Transcription" and "Replication, recombination, and repair." KEGG analysis showed that 17,628 unigenes were involved in 301 pathways. Through comparison of normal and infected transcriptome data, we identified 20 significantly differentially expressed unigenes, which were further confirmed by real-time polymerase chain reaction. Of the 20 unigenes, nine matched the known genes in the database, including three up-regulated genes (virus replicase polyprotein, LRRC3B, and PCK1) and six down-regulated genes (CRP, AICL-like 2, L1CAM, CYB26A1, CHAC1, and ADAM32). The remaining 11 novel unigenes that did not match any known genes in the database may provide a basis for the discovery of new transcripts associated with infection. This study provided a gene expression pattern for normal duck liver and for the previously unrecognized changes in gene transcription that are altered during DHAV-C infection. Our data revealed useful information for future studies on the duck genome and provided new insights into the molecular mechanism of host-DHAV-C interaction.

Depth image enhancement using perceptual texture priors

NASA Astrophysics Data System (ADS)

Bang, Duhyeon; Shim, Hyunjung

2015-03-01

A depth camera is widely used in various applications because it provides a depth image of the scene in real time. However, due to the limited power consumption, the depth camera presents severe noises, incapable of providing the high quality 3D data. Although the smoothness prior is often employed to subside the depth noise, it discards the geometric details so to degrade the distance resolution and hinder achieving the realism in 3D contents. In this paper, we propose a perceptual-based depth image enhancement technique that automatically recovers the depth details of various textures, using a statistical framework inspired by human mechanism of perceiving surface details by texture priors. We construct the database composed of the high quality normals. Based on the recent studies in human visual perception (HVP), we select the pattern density as a primary feature to classify textures. Upon the classification results, we match and substitute the noisy input normals with high quality normals in the database. As a result, our method provides the high quality depth image preserving the surface details. We expect that our work is effective to enhance the details of depth image from 3D sensors and to provide a high-fidelity virtual reality experience.

Pathological speech signal analysis and classification using empirical mode decomposition.

PubMed

Kaleem, Muhammad; Ghoraani, Behnaz; Guergachi, Aziz; Krishnan, Sridhar

2013-07-01

Automated classification of normal and pathological speech signals can provide an objective and accurate mechanism for pathological speech diagnosis, and is an active area of research. A large part of this research is based on analysis of acoustic measures extracted from sustained vowels. However, sustained vowels do not reflect real-world attributes of voice as effectively as continuous speech, which can take into account important attributes of speech such as rapid voice onset and termination, changes in voice frequency and amplitude, and sudden discontinuities in speech. This paper presents a methodology based on empirical mode decomposition (EMD) for classification of continuous normal and pathological speech signals obtained from a well-known database. EMD is used to decompose randomly chosen portions of speech signals into intrinsic mode functions, which are then analyzed to extract meaningful temporal and spectral features, including true instantaneous features which can capture discriminative information in signals hidden at local time-scales. A total of six features are extracted, and a linear classifier is used with the feature vector to classify continuous speech portions obtained from a database consisting of 51 normal and 161 pathological speakers. A classification accuracy of 95.7 % is obtained, thus demonstrating the effectiveness of the methodology.

The normalization heuristic: an untested hypothesis that may misguide medical decisions.

PubMed

Aberegg, Scott K; O'Brien, James M

2009-06-01

Medical practice is increasingly informed by the evidence from randomized controlled trials. When such evidence is not available, clinical hypotheses based on pathophysiological reasoning and common sense guide clinical decision making. One commonly utilized general clinical hypothesis is the assumption that normalizing abnormal laboratory values and physiological parameters will lead to improved patient outcomes. We refer to the general use of this clinical hypothesis to guide medical therapeutics as the "normalization heuristic". In this paper, we operationally define this heuristic and discuss its limitations as a rule of thumb for clinical decision making. We review historical and contemporaneous examples of normalization practices as empirical evidence for the normalization heuristic and to highlight its frailty as a guide for clinical decision making.

Longitudinal Development of Distortion Product Otoacoustic Emissions in Infants With Normal Hearing.

PubMed

Hunter, Lisa L; Blankenship, Chelsea M; Keefe, Douglas H; Feeney, M Patrick; Brown, David K; McCune, Annie; Fitzpatrick, Denis F; Lin, Li

2018-01-23

The purpose of this study was to describe normal characteristics of distortion product otoacoustic emission (DPOAE) signal and noise level in a group of newborns and infants with normal hearing followed longitudinally from birth to 15 months of age. This is a prospective, longitudinal study of 231 infants who passed newborn hearing screening and were verified to have normal hearing. Infants were enrolled from a well-baby nursery and two neonatal intensive care units (NICUs) in Cincinnati, OH. Normal hearing was confirmed with threshold auditory brainstem response and visual reinforcement audiometry. DPOAEs were measured in up to four study visits over the first year after birth. Stimulus frequencies f1 and f2 were used with f2/f1 = 1.22, and the DPOAE was recorded at frequency 2f1-f2. A longitudinal repeated-measure linear mixed model design was used to study changes in DPOAE level and noise level as related to age, middle ear transfer, race, and NICU history. Significant changes in the DPOAE and noise levels occurred from birth to 12 months of age. DPOAE levels were the highest at 1 month of age. The largest decrease in DPOAE level occurred between 1 and 5 months of age in the mid to high frequencies (2 to 8 kHz) with minimal changes occurring between 6, 9, and 12 months of age. The decrease in DPOAE level was significantly related to a decrease in wideband absorbance at the same f2 frequencies. DPOAE noise level increased only slightly with age over the first year with the highest noise levels in the 12-month-old age range. Minor, nonsystematic effects for NICU history, race, and gestational age at birth were found, thus these results were generalizable to commonly seen clinical populations. DPOAE levels were related to wideband middle ear absorbance changes in this large sample of infants confirmed to have normal hearing at auditory brainstem response and visual reinforcement audiometry testing. This normative database can be used to evaluate clinical results from birth to 1 year of age. The distributions of DPOAE level and signal to noise ratio data reported herein across frequency and age in normal-hearing infants who were healthy or had NICU histories may be helpful to detect the presence of hearing loss in infants.

Monitoring by Use of Clusters of Sensor-Data Vectors

NASA Technical Reports Server (NTRS)

Iverson, David L.

2007-01-01

The inductive monitoring system (IMS) is a system of computer hardware and software for automated monitoring of the performance, operational condition, physical integrity, and other aspects of the health of a complex engineering system (e.g., an industrial process line or a spacecraft). The input to the IMS consists of streams of digitized readings from sensors in the monitored system. The IMS determines the type and amount of any deviation of the monitored system from a nominal or normal ( healthy ) condition on the basis of a comparison between (1) vectors constructed from the incoming sensor data and (2) corresponding vectors in a database of nominal or normal behavior. The term inductive reflects the use of a process reminiscent of traditional mathematical induction to learn about normal operation and build the nominal-condition database. The IMS offers two major advantages over prior computational monitoring systems: The computational burden of the IMS is significantly smaller, and there is no need for abnormal-condition sensor data for training the IMS to recognize abnormal conditions. The figure schematically depicts the relationships among the computational processes effected by the IMS. Training sensor data are gathered during normal operation of the monitored system, detailed computational simulation of operation of the monitored system, or both. The training data are formed into vectors that are used to generate the database. The vectors in the database are clustered into regions that represent normal or nominal operation. Once the database has been generated, the IMS compares the vectors of incoming sensor data with vectors representative of the clusters. The monitored system is deemed to be operating normally or abnormally, depending on whether the vector of incoming sensor data is or is not, respectively, sufficiently close to one of the clusters. For this purpose, a distance between two vectors is calculated by a suitable metric (e.g., Euclidean distance) and "sufficiently close" signifies lying at a distance less than a specified threshold value. It must be emphasized that although the IMS is intended to detect off-nominal or abnormal performance or health, it is not necessarily capable of performing a thorough or detailed diagnosis. Limited diagnostic information may be available under some circumstances. For example, the distance of a vector of incoming sensor data from the nearest cluster could serve as an indication of the severity of a malfunction. The identity of the nearest cluster may be a clue as to the identity of the malfunctioning component or subsystem. It is possible to decrease the IMS computation time by use of a combination of cluster-indexing and -retrieval methods. For example, in one method, the distances between each cluster and two or more reference vectors can be used for the purpose of indexing and retrieval. The clusters are sorted into a list according to these distance values, typically in ascending order of distance. When a set of input data arrives and is to be tested, the data are first arranged as an ordered set (that is, a vector). The distances from the input vector to the reference points are computed. The search of clusters from the list can then be limited to those clusters lying within a certain distance range from the input vector; the computation time is reduced by not searching the clusters at a greater distance.

Medical Image Databases

PubMed Central

Tagare, Hemant D.; Jaffe, C. Carl; Duncan, James

1997-01-01

Abstract Information contained in medical images differs considerably from that residing in alphanumeric format. The difference can be attributed to four characteristics: (1) the semantics of medical knowledge extractable from images is imprecise; (2) image information contains form and spatial data, which are not expressible in conventional language; (3) a large part of image information is geometric; (4) diagnostic inferences derived from images rest on an incomplete, continuously evolving model of normality. This paper explores the differentiating characteristics of text versus images and their impact on design of a medical image database intended to allow content-based indexing and retrieval. One strategy for implementing medical image databases is presented, which employs object-oriented iconic queries, semantics by association with prototypes, and a generic schema. PMID:9147338

Longitudinal driver model and collision warning and avoidance algorithms based on human driving databases

NASA Astrophysics Data System (ADS)

Lee, Kangwon

Intelligent vehicle systems, such as Adaptive Cruise Control (ACC) or Collision Warning/Collision Avoidance (CW/CA), are currently under development, and several companies have already offered ACC on selected models. Control or decision-making algorithms of these systems are commonly evaluated under extensive computer simulations and well-defined scenarios on test tracks. However, they have rarely been validated with large quantities of naturalistic human driving data. This dissertation utilized two University of Michigan Transportation Research Institute databases (Intelligent Cruise Control Field Operational Test and System for Assessment of Vehicle Motion Environment) in the development and evaluation of longitudinal driver models and CW/CA algorithms. First, to examine how drivers normally follow other vehicles, the vehicle motion data from the databases were processed using a Kalman smoother. The processed data was then used to fit and evaluate existing longitudinal driver models (e.g., the linear follow-the-leader model, the Newell's special model, the nonlinear follow-the-leader model, the linear optimal control model, the Gipps model and the optimal velocity model). A modified version of the Gipps model was proposed and found to be accurate in both microscopic (vehicle) and macroscopic (traffic) senses. Second, to examine emergency braking behavior and to evaluate CW/CA algorithms, the concepts of signal detection theory and a performance index suitable for unbalanced situations (few threatening data points vs. many safe data points) are introduced. Selected existing CW/CA algorithms were found to have a performance index (geometric mean of true-positive rate and precision) not exceeding 20%. To optimize the parameters of the CW/CA algorithms, a new numerical optimization scheme was developed to replace the original data points with their representative statistics. A new CW/CA algorithm was proposed, which was found to score higher than 55% in the performance index. This dissertation provides a model of how drivers follow lead-vehicles that is much more accurate than other models in the literature. Furthermore, the data-based approach was used to confirm that a CW/CA algorithm utilizing lead-vehicle braking was substantially more effective than existing algorithms, leading to collision warning systems that are much more likely to contribute to driver safety.

Oracle Database 10g: a platform for BLAST search and Regular Expression pattern matching in life sciences

PubMed Central

Stephens, Susie M.; Chen, Jake Y.; Davidson, Marcel G.; Thomas, Shiby; Trute, Barry M.

2005-01-01

As database management systems expand their array of analytical functionality, they become powerful research engines for biomedical data analysis and drug discovery. Databases can hold most of the data types commonly required in life sciences and consequently can be used as flexible platforms for the implementation of knowledgebases. Performing data analysis in the database simplifies data management by minimizing the movement of data from disks to memory, allowing pre-filtering and post-processing of datasets, and enabling data to remain in a secure, highly available environment. This article describes the Oracle Database 10g implementation of BLAST and Regular Expression Searches and provides case studies of their usage in bioinformatics. http://www.oracle.com/technology/software/index.html PMID:15608287

Databases and coordinated research projects at the IAEA on atomic processes in plasmas

NASA Astrophysics Data System (ADS)

Braams, Bastiaan J.; Chung, Hyun-Kyung

2012-05-01

The Atomic and Molecular Data Unit at the IAEA works with a network of national data centres to encourage and coordinate production and dissemination of fundamental data for atomic, molecular and plasma-material interaction (A+M/PMI) processes that are relevant to the realization of fusion energy. The Unit maintains numerical and bibliographical databases and has started a Wiki-style knowledge base. The Unit also contributes to A+M database interface standards and provides a search engine that offers a common interface to multiple numerical A+M/PMI databases. Coordinated Research Projects (CRPs) bring together fusion energy researchers and atomic, molecular and surface physicists for joint work towards the development of new data and new methods. The databases and current CRPs on A+M/PMI processes are briefly described here.

Cost differential by site of service for cancer patients receiving chemotherapy.

PubMed

Hayes, Jad; Hoverman, Russell J; Brow, Matthew E; Dilbeck, Dana C; Verrilli, Diana K; Garey, Jody; Espirito, Janet L; Cardona, Jorge; Beveridge, Roy

2015-03-01

To compare the costs of: 1) chemotherapy treatment across clinical, demographic, and geographic variables; and 2) various cancer care-related cost categories between patients receiving chemotherapy in a community oncology versus a hospital outpatient setting. Data from the calendar years 2008 to 2010 from the Truven Health Analytics MarketScan Commercial Claims and Encounters Database were analyzed. During 2010, the data set contained approximately 45 million unique commercially insured patients with 70,984 cancer patients receiving chemotherapy. These patients were assigned to cohorts depending on whether they received chemotherapy at a community oncology or hospital outpatient setting. Cost data for 9 common cancer types were extracted from the database and analyzed on a per member per month basis to normalize costs; costs included amounts paid by the payer and patient payment. Community oncology and hospital outpatient setting chemotherapy treatment costs were categorized and examined according to cancer diagnosis, patient demographics, and geographic location. Patients receiving chemotherapy treatment in the community oncology clinic had a 20% to 39% lower mean per member per month cost of care, depending on diagnosis, compared with those receiving chemotherapy in the hospital outpatient setting. This cost differential was consistent across cancer type, geographic location, patient age, and number of chemotherapy sessions. Various cost categories examined were also higher for those treated in the hospital outpatient setting. The cost of care for patients receiving chemotherapy was consistently lower in the community oncology clinic compared with the hospital outpatient setting, controlling for the clinical, demographic, and geographic variables analyzed.

[Effect of vinegar-processed Curcumae Rhizoma on bile metabolism in rats].

PubMed

Gu, Wei; Lu, Tu-Lin; Li, Jin-Ci; Wang, Qiao-Han; Pan, Zi-Hao; Ji, De; Li, Lin; Zhang, Ji; Mao, Chun-Qin

2016-04-01

To explore the effect of vinegar-processed Curcumae Rhizoma on endogenous metabolites in bile by investigating the endogenous metabolites difference in bile before and after Curcumae Rhizoma was processed with vinegar. Alcohol extracts of crude and vinegar-processed Curcumae Rhizoma, as well as normal saline were prepared respectively, which were then given to the rats by intragastric administration for 0.5 h. Then common bile duct intubation drainage was conducted to collect 12 h bile of the rats. UPLC-TOF-MS analysis of bile samples was applied after 1∶3 acetonitrile protein precipitation; unidimensional statistics were combined with multivariate statistics and PeakView software was compared with network database to identify the potential biomarkers. Vinegar-processed Curcumae Rhizoma extracts had significant effects on metabolites spectrum in bile of the rats. With the boundaries of P<0.05, 13 metabolites with significant differences were found in bile of crude and vinegar-processed Curcumae Rhizoma groups, and 8 of them were identified when considering the network database. T-test unidimensional statistical analysis was applied between administration groups and blank group to obtain 7 metabolites with significant differences and identify them as potential biomarkers. 6 of the potential biomarkers were up-regulated in vinegar-processed group, which were related to the metabolism regulation of phospholipid metabolism, fat metabolism, bile acid metabolism, and N-acylethanolamine hydrolysis reaction balance, indicating the mechanism of vinegar-processed Curcumae Rhizoma on endogenous metabolites in bile of the rats. Copyright© by the Chinese Pharmaceutical Association.

Investigation of Maternal Genotype Effects in Autism by Genome-Wide Association

PubMed Central

Yuan, Han; Dougherty, Joseph D.

2014-01-01

Lay Abstract Autism spectrum disorders (ASDs) are pervasive developmental disorders which have both a genetic and environmental component. One source of the environmental component is the in utero (prenatal) environment. The maternal genome can potentially contribute to the risk of autism in children by altering this prenatal environment. In this study, the possibility of maternal genotype effects was explored by looking for common variants (single nucleotide polymorphisms, or SNPs) in the maternal genome associated with increased risk of autism in children. We performed a case/control genome-wide association study (GWAS) using mothers of probands as cases and either fathers of probands or normal females as controls, using two collections of families with autism. We did not identify any SNP that reached significance and thus a common variant of large effect is unlikely. However, there was evidence for the possibility of a large number of alleles each carrying a small effect. This suggested that if there is a contribution to autism risk through common-variant maternal genetic effects, it may be the result of multiple loci of small effects. We did not investigate rare variants in this study. Scientific Abstract Like most psychiatric disorders, autism spectrum disorders have both a genetic and an environmental component. While previous studies have clearly demonstrated the contribution of in utero (prenatal) environment on autism risk, most of them focused on transient environmental factors. Based on a recent sibling study, we hypothesized that environmental factors could also come from the maternal genome, which would result in persistent effects across siblings. In this study, the possibility of maternal genotype effects was examined by looking for common variants (single nucleotide polymorphisms, or SNPs) in the maternal genome associated with increased risk of autism in children. A case/control genome-wide association study (GWAS) was performed using mothers of probands as cases and either fathers of probands or normal females as controls. Autism Genetic Resource Exchange (AGRE) and Illumina Genotype Control Database (iCon) were used as our discovery cohort (n=1616). The same analysis was then replicated on Simon Simplex Collection (SSC) and Study of Addiction: Genetics and Environment (SAGE) datasets (n=2732). We did not identify any SNP that reached genome-wide significance (p<10−8) and thus a common variant of large effect is unlikely. However, there was evidence for the possibility of a large number of alleles of effective size marginally below our power to detect. PMID:24574247

Systematic gene microarray analysis of the lncRNA expression profiles in human uterine cervix carcinoma.

PubMed

Chen, Jie; Fu, Ziyi; Ji, Chenbo; Gu, Pingqing; Xu, Pengfei; Yu, Ningzhu; Kan, Yansheng; Wu, Xiaowei; Shen, Rong; Shen, Yan

2015-05-01

The human uterine cervix carcinoma is one of the most well-known malignancy reproductive system cancers, which threatens women health globally. However, the mechanisms of the oncogenesis and development process of cervix carcinoma are not yet fully understood. Long non-coding RNAs (lncRNAs) have been proved to play key roles in various biological processes, especially development of cancer. The function and mechanism of lncRNAs on cervix carcinoma is still rarely reported. We selected 3 cervix cancer and normal cervix tissues separately, then performed lncRNA microarray to detect the differentially expressed lncRNAs. Subsequently, we explored the potential function of these dysregulated lncRNAs through online bioinformatics databases. Finally, quantity real-time PCR was carried out to confirm the expression levels of these dysregulated lncRNAs in cervix cancer and normal tissues. We uncovered the profiles of differentially expressed lncRNAs between normal and cervix carcinoma tissues by using the microarray techniques, and found 1622 upregulated and 3026 downregulated lncRNAs (fold-change>2.0) in cervix carcinoma compared to the normal cervical tissue. Furthermore, we found HOXA11-AS might participate in cervix carcinogenesis by regulating HOXA11, which is involved in regulating biological processes of cervix cancer. This study afforded expression profiles of lncRNAs between cervix carcinoma tissue and normal cervical tissue, which could provide database for further research about the function and mechanism of key-lncRNAs in cervix carcinoma, and might be helpful to explore potential diagnosis factors and therapeutic targets for cervix carcinoma. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

An SQL query generator for CLIPS

NASA Technical Reports Server (NTRS)

Snyder, James; Chirica, Laurian

1990-01-01

As expert systems become more widely used, their access to large amounts of external information becomes increasingly important. This information exists in several forms such as statistical, tabular data, knowledge gained by experts and large databases of information maintained by companies. Because many expert systems, including CLIPS, do not provide access to this external information, much of the usefulness of expert systems is left untapped. The scope of this paper is to describe a database extension for the CLIPS expert system shell. The current industry standard database language is SQL. Due to SQL standardization, large amounts of information stored on various computers, potentially at different locations, will be more easily accessible. Expert systems should be able to directly access these existing databases rather than requiring information to be re-entered into the expert system environment. The ORACLE relational database management system (RDBMS) was used to provide a database connection within the CLIPS environment. To facilitate relational database access a query generation system was developed as a CLIPS user function. The queries are entered in a CLlPS-like syntax and are passed to the query generator, which constructs and submits for execution, an SQL query to the ORACLE RDBMS. The query results are asserted as CLIPS facts. The query generator was developed primarily for use within the ICADS project (Intelligent Computer Aided Design System) currently being developed by the CAD Research Unit in the California Polytechnic State University (Cal Poly). In ICADS, there are several parallel or distributed expert systems accessing a common knowledge base of facts. Expert system has a narrow domain of interest and therefore needs only certain portions of the information. The query generator provides a common method of accessing this information and allows the expert system to specify what data is needed without specifying how to retrieve it.

Common variants in Mendelian kidney disease genes and their association with renal function.

PubMed

Parsa, Afshin; Fuchsberger, Christian; Köttgen, Anna; O'Seaghdha, Conall M; Pattaro, Cristian; de Andrade, Mariza; Chasman, Daniel I; Teumer, Alexander; Endlich, Karlhans; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Kim, Young J; Taliun, Daniel; Li, Man; Feitosa, Mary; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C; Glazer, Nicole; Isaacs, Aaron; Rao, Madhumathi; Smith, Albert V; O'Connell, Jeffrey R; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Hwang, Shih-Jen; Atkinson, Elizabeth J; Lohman, Kurt; Cornelis, Marilyn C; Johansson, Asa; Tönjes, Anke; Dehghan, Abbas; Couraki, Vincent; Holliday, Elizabeth G; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y; Murgia, Federico; Trompet, Stella; Imboden, Medea; Kollerits, Barbara; Pistis, Giorgio; Harris, Tamara B; Launer, Lenore J; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D; Boerwinkle, Eric; Schmidt, Helena; Hofer, Edith; Hu, Frank; Demirkan, Ayse; Oostra, Ben A; Turner, Stephen T; Ding, Jingzhong; Andrews, Jeanette S; Freedman, Barry I; Giulianini, Franco; Koenig, Wolfgang; Illig, Thomas; Döring, Angela; Wichmann, H-Erich; Zgaga, Lina; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H; Wright, Alan F; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G; Rivadeneira, Fernando; Aulchenko, Yurii S; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Stengel, Bénédicte; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Krämer, Bernhard K; Portas, Laura; Ford, Ian; Buckley, Brendan M; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Mitchell, Paul; Ciullo, Marina; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J Wouter; Probst-Hensch, Nicole M; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; van Duijn, Cornelia M; Borecki, Ingrid; Kardia, Sharon L R; Liu, Yongmei; Curhan, Gary C; Rudan, Igor; Gyllensten, Ulf; Wilson, James F; Franke, Andre; Pramstaller, Peter P; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline; Hayward, Caroline; Ridker, Paul M; Bochud, Murielle; Heid, Iris M; Siscovick, David S; Fox, Caroline S; Kao, W Linda; Böger, Carsten A

2013-12-01

Many common genetic variants identified by genome-wide association studies for complex traits map to genes previously linked to rare inherited Mendelian disorders. A systematic analysis of common single-nucleotide polymorphisms (SNPs) in genes responsible for Mendelian diseases with kidney phenotypes has not been performed. We thus developed a comprehensive database of genes for Mendelian kidney conditions and evaluated the association between common genetic variants within these genes and kidney function in the general population. Using the Online Mendelian Inheritance in Man database, we identified 731 unique disease entries related to specific renal search terms and confirmed a kidney phenotype in 218 of these entries, corresponding to mutations in 258 genes. We interrogated common SNPs (minor allele frequency >5%) within these genes for association with the estimated GFR in 74,354 European-ancestry participants from the CKDGen Consortium. However, the top four candidate SNPs (rs6433115 at LRP2, rs1050700 at TSC1, rs249942 at PALB2, and rs9827843 at ROBO2) did not achieve significance in a stage 2 meta-analysis performed in 56,246 additional independent individuals, indicating that these common SNPs are not associated with estimated GFR. The effect of less common or rare variants in these genes on kidney function in the general population and disease-specific cohorts requires further research.

Ventilator-Related Adverse Events: A Taxonomy and Findings From 3 Incident Reporting Systems.

PubMed

Pham, Julius Cuong; Williams, Tamara L; Sparnon, Erin M; Cillie, Tam K; Scharen, Hilda F; Marella, William M

2016-05-01

In 2009, researchers from Johns Hopkins University's Armstrong Institute for Patient Safety and Quality; public agencies, including the FDA; and private partners, including the Emergency Care Research Institute and the University HealthSystem Consortium (UHC) Safety Intelligence Patient Safety Organization, sought to form a public-private partnership for the promotion of patient safety (P5S) to advance patient safety through voluntary partnerships. The study objective was to test the concept of the P5S to advance our understanding of safety issues related to ventilator events, to develop a common classification system for categorizing adverse events related to mechanical ventilators, and to perform a comparison of adverse events across different adverse event reporting systems. We performed a cross-sectional analysis of ventilator-related adverse events reported in 2012 from the following incident reporting systems: the Pennsylvania Patient Safety Authority's Patient Safety Reporting System, UHC's Safety Intelligence Patient Safety Organization database, and the FDA's Manufacturer and User Facility Device Experience database. Once each organization had its dataset of ventilator-related adverse events, reviewers read the narrative descriptions of each event and classified it according to the developed common taxonomy. A Pennsylvania Patient Safety Authority, FDA, and UHC search provided 252, 274, and 700 relevant reports, respectively. The 3 event types most commonly reported to the UHC and the Pennsylvania Patient Safety Authority's Patient Safety Reporting System databases were airway/breathing circuit issue, human factor issues, and ventilator malfunction events. The top 3 event types reported to the FDA were ventilator malfunction, power source issue, and alarm failure. Overall, we found that (1) through the development of a common taxonomy, adverse events from 3 reporting systems can be evaluated, (2) the types of events reported in each database were related to the purpose of the database and the source of the reports, resulting in significant differences in reported event categories across the 3 systems, and (3) a public-private collaboration for investigating ventilator-related adverse events under the P5S model is feasible. Copyright © 2016 by Daedalus Enterprises.

Establishing Emissions Representative of Normal Source Operation for Furnace E, Owens-Brockway Glass Container, Inc., Atlanta, Georgia

EPA Pesticide Factsheets

This document may be of assistance in applying the New Source Review (NSR) air permitting regulations including the Prevention of Significant Deterioration (PSD) requirements. This document is part of the NSR Policy and Guidance Database. Some documents in the database are a scanned or retyped version of a paper photocopy of the original. Although we have taken considerable effort to quality assure the documents, some may contain typographical errors. Contact the office that issued the document if you need a copy of the original.

Tissue Molecular Anatomy Project (TMAP): an expression database for comparative cancer proteomics.

PubMed

Medjahed, Djamel; Luke, Brian T; Tontesh, Tawady S; Smythers, Gary W; Munroe, David J; Lemkin, Peter F

2003-08-01

By mining publicly accessible databases, we have developed a collection of tissue-specific predictive protein expression maps as a function of cancer histological state. Data analysis is applied to the differential expression of gene products in pooled libraries from the normal to the altered state(s). We wish to report the initial results of our survey across different tissues and explore the extent to which this comparative approach may help uncover panels of potential biomarkers of tumorigenesis which would warrant further examination in the laboratory.

Differentiation of several interstitial lung disease patterns in HRCT images using support vector machine: role of databases on performance

NASA Astrophysics Data System (ADS)

Kale, Mandar; Mukhopadhyay, Sudipta; Dash, Jatindra K.; Garg, Mandeep; Khandelwal, Niranjan

2016-03-01

Interstitial lung disease (ILD) is complicated group of pulmonary disorders. High Resolution Computed Tomography (HRCT) considered to be best imaging technique for analysis of different pulmonary disorders. HRCT findings can be categorised in several patterns viz. Consolidation, Emphysema, Ground Glass Opacity, Nodular, Normal etc. based on their texture like appearance. Clinician often find it difficult to diagnosis these pattern because of their complex nature. In such scenario computer-aided diagnosis system could help clinician to identify patterns. Several approaches had been proposed for classification of ILD patterns. This includes computation of textural feature and training /testing of classifier such as artificial neural network (ANN), support vector machine (SVM) etc. In this paper, wavelet features are calculated from two different ILD database, publically available MedGIFT ILD database and private ILD database, followed by performance evaluation of ANN and SVM classifiers in terms of average accuracy. It is found that average classification accuracy by SVM is greater than ANN where trained and tested on same database. Investigation continued further to test variation in accuracy of classifier when training and testing is performed with alternate database and training and testing of classifier with database formed by merging samples from same class from two individual databases. The average classification accuracy drops when two independent databases used for training and testing respectively. There is significant improvement in average accuracy when classifiers are trained and tested with merged database. It infers dependency of classification accuracy on training data. It is observed that SVM outperforms ANN when same database is used for training and testing.

Dimensional modeling: beyond data processing constraints.

PubMed

Bunardzic, A

1995-01-01

The focus of information processing requirements is shifting from the on-line transaction processing (OLTP) issues to the on-line analytical processing (OLAP) issues. While the former serves to ensure the feasibility of the real-time on-line transaction processing (which has already exceeded a level of up to 1,000 transactions per second under normal conditions), the latter aims at enabling more sophisticated analytical manipulation of data. The OLTP requirements, or how to efficiently get data into the system, have been solved by applying the Relational theory in the form of Entity-Relation model. There is presently no theory related to OLAP that would resolve the analytical processing requirements as efficiently as Relational theory provided for the transaction processing. The "relational dogma" also provides the mathematical foundation for the Centralized Data Processing paradigm in which mission-critical information is incorporated as 'one and only one instance' of data, thus ensuring data integrity. In such surroundings, the information that supports business analysis and decision support activities is obtained by running predefined reports and queries that are provided by the IS department. In today's intensified competitive climate, businesses are finding that this traditional approach is not good enough. The only way to stay on top of things, and to survive and prosper, is to decentralize the IS services. The newly emerging Distributed Data Processing, with its increased emphasis on empowering the end user, does not seem to find enough merit in the relational database model to justify relying upon it. Relational theory proved too rigid and complex to accommodate the analytical processing needs. In order to satisfy the OLAP requirements, or how to efficiently get the data out of the system, different models, metaphors, and theories have been devised. All of them are pointing to the need for simplifying the highly non-intuitive mathematical constraints found in the relational databases normalized to their 3rd normal form. Object-oriented approach insists on the importance of the common sense component of the data processing activities. But, particularly interesting, is the approach that advocates the necessity of 'flattening' the structure of the business models as we know them today. This discipline is called Dimensional Modeling and it enables users to form multidimensional views of the relevant facts which are stored in a 'flat' (non-structured), easy-to-comprehend and easy-to-access database. When using dimensional modeling, we relax many of the axioms inherent in a relational model. We focus on the knowledge of the relevant facts which are reflecting the business operations and are the real basis for the decision support and business analysis. At the core of the dimensional modeling are fact tables that contain the non-discrete, additive data. To determine the level of aggregation of these facts, we use granularity tables that specify the resolution, or the level/detail, that the user is allowed to entertain. The third component is dimension tables that embody the knowledge of the constraints to be used to form the views.

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

PubMed Central

2013-01-01

Background System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. Results Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. Conclusions Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr. PMID:23586463

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool.

PubMed

Chen, Edward Y; Tan, Christopher M; Kou, Yan; Duan, Qiaonan; Wang, Zichen; Meirelles, Gabriela Vaz; Clark, Neil R; Ma'ayan, Avi

2013-04-15

System-wide profiling of genes and proteins in mammalian cells produce lists of differentially expressed genes/proteins that need to be further analyzed for their collective functions in order to extract new knowledge. Once unbiased lists of genes or proteins are generated from such experiments, these lists are used as input for computing enrichment with existing lists created from prior knowledge organized into gene-set libraries. While many enrichment analysis tools and gene-set libraries databases have been developed, there is still room for improvement. Here, we present Enrichr, an integrative web-based and mobile software application that includes new gene-set libraries, an alternative approach to rank enriched terms, and various interactive visualization approaches to display enrichment results using the JavaScript library, Data Driven Documents (D3). The software can also be embedded into any tool that performs gene list analysis. We applied Enrichr to analyze nine cancer cell lines by comparing their enrichment signatures to the enrichment signatures of matched normal tissues. We observed a common pattern of up regulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interlukin signaling in K562 cells when compared with normal myeloid CD33+ cells. Such analyses provide global visualization of critical differences between normal tissues and cancer cell lines but can be applied to many other scenarios. Enrichr is an easy to use intuitive enrichment analysis web-based tool providing various types of visualization summaries of collective functions of gene lists. Enrichr is open source and freely available online at: http://amp.pharm.mssm.edu/Enrichr.

Relationship of Echocardiographic Z Scores Adjusted for Body Surface Area to Age, Sex, Race, and Ethnicity: The Pediatric Heart Network Normal Echocardiogram Database.

PubMed

Lopez, Leo; Colan, Steven; Stylianou, Mario; Granger, Suzanne; Trachtenberg, Felicia; Frommelt, Peter; Pearson, Gail; Camarda, Joseph; Cnota, James; Cohen, Meryl; Dragulescu, Andreea; Frommelt, Michele; Garuba, Olukayode; Johnson, Tiffanie; Lai, Wyman; Mahgerefteh, Joseph; Pignatelli, Ricardo; Prakash, Ashwin; Sachdeva, Ritu; Soriano, Brian; Soslow, Jonathan; Spurney, Christopher; Srivastava, Shubhika; Taylor, Carolyn; Thankavel, Poonam; van der Velde, Mary; Minich, LuAnn

2017-11-01

Published nomograms of pediatric echocardiographic measurements are limited by insufficient sample size to assess the effects of age, sex, race, and ethnicity. Variable methodologies have resulted in a wide range of Z scores for a single measurement. This multicenter study sought to determine Z scores for common measurements adjusted for body surface area (BSA) and stratified by age, sex, race, and ethnicity. Data collected from healthy nonobese children ≤18 years of age at 19 centers with a normal echocardiogram included age, sex, race, ethnicity, height, weight, echocardiographic images, and measurements performed at the Core Laboratory. Z score models involved indexed parameters (X/BSA α ) that were normally distributed without residual dependence on BSA. The models were tested for the effects of age, sex, race, and ethnicity. Raw measurements from models with and without these effects were compared, and <5% difference was considered clinically insignificant because interobserver variability for echocardiographic measurements are reported as ≥5% difference. Of the 3566 subjects, 90% had measurable images. Appropriate BSA transformations (BSA α ) were selected for each measurement. Multivariable regression revealed statistically significant effects by age, sex, race, and ethnicity for all outcomes, but all effects were clinically insignificant based on comparisons of models with and without the effects, resulting in Z scores independent of age, sex, race, and ethnicity for each measurement. Echocardiographic Z scores based on BSA were derived from a large, diverse, and healthy North American population. Age, sex, race, and ethnicity have small effects on the Z scores that are statistically significant but not clinically important. © 2017 American Heart Association, Inc.

Linking U.S. School District Test Score Distributions to a Common Scale. CEPA Working Paper No. 16-09

ERIC Educational Resources Information Center

Reardon, Sean F.; Kalogrides, Demetra; Ho, Andrew D.

2017-01-01

There is no comprehensive database of U.S. district-level test scores that is comparable across states. We describe and evaluate a method for constructing such a database. First, we estimate linear, reliability-adjusted linking transformations from state test score scales to the scale of the National Assessment of Educational Progress (NAEP). We…

VEMAP phase 2 bioclimatic database. I. Gridded historical (20th century) climate for modeling ecosystem dynamics across the conterminous USA

Treesearch

Timothy G.F. Kittel; Nan. A. Rosenbloom; J.A. Royle; C. Daly; W.P. Gibson; H.H. Fisher; P. Thornton; D.N. Yates; S. Aulenbach; C. Kaufman; R. McKeown; Dominque Bachelet; David S. Schimel

2004-01-01

Analysis and simulation of biospheric responses to historical forcing require surface climate data that capture those aspects of climate that control ecological processes, including key spatial gradients and modes of temporal variability. We developed a multivariate, gridded historical climate dataset for the conterminous USA as a common input database for the...

Comparison of machine learning and semi-quantification algorithms for (I123)FP-CIT classification: the beginning of the end for semi-quantification?

PubMed

Taylor, Jonathan Christopher; Fenner, John Wesley

2017-11-29

Semi-quantification methods are well established in the clinic for assisted reporting of (I123) Ioflupane images. Arguably, these are limited diagnostic tools. Recent research has demonstrated the potential for improved classification performance offered by machine learning algorithms. A direct comparison between methods is required to establish whether a move towards widespread clinical adoption of machine learning algorithms is justified. This study compared three machine learning algorithms with that of a range of semi-quantification methods, using the Parkinson's Progression Markers Initiative (PPMI) research database and a locally derived clinical database for validation. Machine learning algorithms were based on support vector machine classifiers with three different sets of features: Voxel intensities Principal components of image voxel intensities Striatal binding radios from the putamen and caudate. Semi-quantification methods were based on striatal binding ratios (SBRs) from both putamina, with and without consideration of the caudates. Normal limits for the SBRs were defined through four different methods: Minimum of age-matched controls Mean minus 1/1.5/2 standard deviations from age-matched controls Linear regression of normal patient data against age (minus 1/1.5/2 standard errors) Selection of the optimum operating point on the receiver operator characteristic curve from normal and abnormal training data Each machine learning and semi-quantification technique was evaluated with stratified, nested 10-fold cross-validation, repeated 10 times. The mean accuracy of the semi-quantitative methods for classification of local data into Parkinsonian and non-Parkinsonian groups varied from 0.78 to 0.87, contrasting with 0.89 to 0.95 for classifying PPMI data into healthy controls and Parkinson's disease groups. The machine learning algorithms gave mean accuracies between 0.88 to 0.92 and 0.95 to 0.97 for local and PPMI data respectively. Classification performance was lower for the local database than the research database for both semi-quantitative and machine learning algorithms. However, for both databases, the machine learning methods generated equal or higher mean accuracies (with lower variance) than any of the semi-quantification approaches. The gain in performance from using machine learning algorithms as compared to semi-quantification was relatively small and may be insufficient, when considered in isolation, to offer significant advantages in the clinical context.

The making of a pan-European organ transplant registry.

PubMed

Smits, Jacqueline M; Niesing, Jan; Breidenbach, Thomas; Collett, Dave

2013-03-01

A European patient registry to track the outcomes of organ transplant recipients does not exist. As knowledge gleaned from large registries has already led to the creation of standards of care that gained widespread support from patients and healthcare providers, the European Union initiated a project that would enable the creation of a European Registry linking currently existing national databases. This report contains a description of all functional, technical, and legal prerequisites, which upon fulfillment should allow for the seamless sharing of national longitudinal data across temporal, geographical, and subspecialty boundaries. To create a platform that can effortlessly link multiple databases and maintain the integrity of the existing national databases crucial elements were described during the project. These elements are: (i) use of a common dictionary, (ii) use of a common database and refined data uploading technology, (iii) use of standard methodology to allow uniform protocol driven and meaningful long-term follow-up analyses, (iv) use of a quality assurance mechanism to guarantee completeness and accuracy of the data collected, and (v) establishment of a solid legal framework that allows for safe data exchange. © 2012 The Authors Transplant International © 2012 European Society for Organ Transplantation. Published by Blackwell Publishing Ltd.

Missing data may lead to changes in hip fracture database studies: a study of the American College of Surgeons National Surgical Quality Improvement Program.

PubMed

Basques, B A; McLynn, R P; Lukasiewicz, A M; Samuel, A M; Bohl, D D; Grauer, J N

2018-02-01

The aims of this study were to characterize the frequency of missing data in the National Surgical Quality Improvement Program (NSQIP) database and to determine how missing data can influence the results of studies dealing with elderly patients with a fracture of the hip. Patients who underwent surgery for a fracture of the hip between 2005 and 2013 were identified from the NSQIP database and the percentage of missing data was noted for demographics, comorbidities and laboratory values. These variables were tested for association with 'any adverse event' using multivariate regressions based on common ways of handling missing data. A total of 26 066 patients were identified. The rate of missing data was up to 77.9% for many variables. Multivariate regressions comparing three methods of handling missing data found different risk factors for postoperative adverse events. Only seven of 35 identified risk factors (20%) were common to all three analyses. Missing data is an important issue in national database studies that researchers must consider when evaluating such investigations. Cite this article: Bone Joint J 2018;100-B:226-32. ©2018 The British Editorial Society of Bone & Joint Surgery.

Wenxin Keli for atrial fibrillation

PubMed Central

He, Zhuogen; Zheng, Minan; Xie, Pingchang; Wang, Yuanping; Yan, Xia; Deng, Dingwei

2018-01-01

Abstract Background: Atrial fibrillation (AF) is a most common cardiac arrhythmia in clinical practice. In China, Wenxin Keli (WXKL) therapy is a common treatment for AF, but its effects and safety remain uncertain. This protocol is to provide the methods used to assess the effectiveness and safety of WXKL for the treatment of patients with AF. Methods: We will search comprehensively the 4 English databases EMBASE, the Cochrane Central Register of Controlled Trials (Cochrane Library), PubMed, and Medline and 3 Chinese databases China National Knowledge Infrastructure (CNKI), Chinese Biomedical Literature Database (CBM), and Chinese Science and Technology Periodical database (VIP) on computer on March 2018 for the randomized controlled trials (RCTs) regarding WXKL for AF. The therapeutic effects according to the sinus rhythm and p-wave dispersion (Pwd) will be accepted as the primary outcomes. We will use RevMan V.5.3 software as well to compute the data synthesis carefully when a meta-analysis is allowed. Results: This study will provide a high-quality synthesis of current evidence of WXKL for AF. Conclusion: The conclusion of our systematic review will provide evidence to judge whether WXKL is an effective intervention for patient with AF. PROSPERO registration number: PROSPERO CRD 42018082045. PMID:29702984

Development of the Lymphoma Enterprise Architecture Database: A caBIG(tm) Silver level compliant System

PubMed Central

Huang, Taoying; Shenoy, Pareen J.; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W.; Flowers, Christopher R.

2009-01-01

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid™ (caBIG™) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system™ (LEAD™), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute’s Center for Bioinformatics to establish the LEAD™ platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD™ could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG™ can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG™ to the management of clinical and biological data. PMID:19492074

Development of the Lymphoma Enterprise Architecture Database: a caBIG Silver level compliant system.

PubMed

Huang, Taoying; Shenoy, Pareen J; Sinha, Rajni; Graiser, Michael; Bumpers, Kevin W; Flowers, Christopher R

2009-04-03

Lymphomas are the fifth most common cancer in United States with numerous histological subtypes. Integrating existing clinical information on lymphoma patients provides a platform for understanding biological variability in presentation and treatment response and aids development of novel therapies. We developed a cancer Biomedical Informatics Grid (caBIG) Silver level compliant lymphoma database, called the Lymphoma Enterprise Architecture Data-system (LEAD), which integrates the pathology, pharmacy, laboratory, cancer registry, clinical trials, and clinical data from institutional databases. We utilized the Cancer Common Ontological Representation Environment Software Development Kit (caCORE SDK) provided by National Cancer Institute's Center for Bioinformatics to establish the LEAD platform for data management. The caCORE SDK generated system utilizes an n-tier architecture with open Application Programming Interfaces, controlled vocabularies, and registered metadata to achieve semantic integration across multiple cancer databases. We demonstrated that the data elements and structures within LEAD could be used to manage clinical research data from phase 1 clinical trials, cohort studies, and registry data from the Surveillance Epidemiology and End Results database. This work provides a clear example of how semantic technologies from caBIG can be applied to support a wide range of clinical and research tasks, and integrate data from disparate systems into a single architecture. This illustrates the central importance of caBIG to the management of clinical and biological data.

Interhospital network system using the worldwide web and the common gateway interface.

PubMed

Oka, A; Harima, Y; Nakano, Y; Tanaka, Y; Watanabe, A; Kihara, H; Sawada, S

1999-05-01

We constructed an interhospital network system using the worldwide web (WWW) and the Common Gateway Interface (CGI). Original clinical images are digitized and stored as a database for educational and research purposes. Personal computers (PCs) are available for data treatment and browsing. Our system is simple, as digitized images are stored into a Unix server machine. Images of important and interesting clinical cases are selected and registered into the image database using CGI. The main image format is 8- or 12-bit Joint Photographic Experts Group (JPEG) image. Original clinical images are finally stored in CD-ROM using a CD recorder. The image viewer can browse all of the images for one case at once as thumbnail pictures; image quality can be selected depending on the user's purpose. Using the network system, clinical images of interesting cases can be rapidly transmitted and discussed with other related hospitals. Data transmission from relational hospitals takes 1 to 2 minutes per 500 Kbyte of data. More distant hospitals (e.g., Rakusai Hospital, Kyoto) takes 1 minute more. The mean number of accesses our image database in a recent 3-month period was 470. There is a total about 200 cases in our image database, acquired over the past 2 years. Our system is useful for communication and image treatment between hospitals and we will describe the elements of our system and image database.

Clinical canine dental radiography.

PubMed

Bannon, Kristin M

2013-05-01

The purpose of this article is to provide small animal veterinarians in private practice a guideline for interpretation of the most common findings in canine intraoral radiology. Normal oral and dental anatomy is presented. A brief review of variations of normal, common periodontal and endodontic pathology findings and developmental anomalies is provided. Copyright © 2013 Elsevier Inc. All rights reserved.

Drug-Path: a database for drug-induced pathways.

PubMed

Zeng, Hui; Qiu, Chengxiang; Cui, Qinghua

2015-01-01

Some databases for drug-associated pathways have been built and are publicly available. However, the pathways curated in most of these databases are drug-action or drug-metabolism pathways. In recent years, high-throughput technologies such as microarray and RNA-sequencing have produced lots of drug-induced gene expression profiles. Interestingly, drug-induced gene expression profile frequently show distinct patterns, indicating that drugs normally induce the activation or repression of distinct pathways. Therefore, these pathways contribute to study the mechanisms of drugs and drug-repurposing. Here, we present Drug-Path, a database of drug-induced pathways, which was generated by KEGG pathway enrichment analysis for drug-induced upregulated genes and downregulated genes based on drug-induced gene expression datasets in Connectivity Map. Drug-Path provides user-friendly interfaces to retrieve, visualize and download the drug-induced pathway data in the database. In addition, the genes deregulated by a given drug are highlighted in the pathways. All data were organized using SQLite. The web site was implemented using Django, a Python web framework. Finally, we believe that this database will be useful for related researches. © The Author(s) 2015. Published by Oxford University Press.

Python and computer vision

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

Doak, J. E.; Prasad, Lakshman

2002-01-01

This paper discusses the use of Python in a computer vision (CV) project. We begin by providing background information on the specific approach to CV employed by the project. This includes a brief discussion of Constrained Delaunay Triangulation (CDT), the Chordal Axis Transform (CAT), shape feature extraction and syntactic characterization, and normalization of strings representing objects. (The terms 'object' and 'blob' are used interchangeably, both referring to an entity extracted from an image.) The rest of the paper focuses on the use of Python in three critical areas: (1) interactions with a MySQL database, (2) rapid prototyping of algorithms, andmore » (3) gluing together all components of the project including existing C and C++ modules. For (l), we provide a schema definition and discuss how the various tables interact to represent objects in the database as tree structures. (2) focuses on an algorithm to create a hierarchical representation of an object, given its string representation, and an algorithm to match unknown objects against objects in a database. And finally, (3) discusses the use of Boost Python to interact with the pre-existing C and C++ code that creates the CDTs and CATS, performs shape feature extraction and syntactic characterization, and normalizes object strings. The paper concludes with a vision of the future use of Python for the CV project.« less

Impact of database quality in knowledge-based treatment planning for prostate cancer.

PubMed

Wall, Phillip D H; Carver, Robert L; Fontenot, Jonas D

2018-03-13

This article investigates dose-volume prediction improvements in a common knowledge-based planning (KBP) method using a Pareto plan database compared with using a conventional, clinical plan database. Two plan databases were created using retrospective, anonymized data of 124 volumetric modulated arc therapy (VMAT) prostate cancer patients. The clinical plan database (CPD) contained planning data from each patient's clinically treated VMAT plan, which were manually optimized by various planners. The multicriteria optimization database (MCOD) contained Pareto-optimal plan data from VMAT plans created using a standardized multicriteria optimization protocol. Overlap volume histograms, incorporating fractional organ at risk volumes only within the treatment fields, were computed for each patient and used to match new patient anatomy to similar database patients. For each database patient, CPD and MCOD KBP predictions were generated for D 10 , D 30 , D 50 , D 65 , and D 80 of the bladder and rectum in a leave-one-out manner. Prediction achievability was evaluated through a replanning study on a subset of 31 randomly selected database patients using the best KBP predictions, regardless of plan database origin, as planning goals. MCOD predictions were significantly lower than CPD predictions for all 5 bladder dose-volumes and rectum D 50 (P = .004) and D 65 (P < .001), whereas CPD predictions for rectum D 10 (P = .005) and D 30 (P < .001) were significantly less than MCOD predictions. KBP predictions were statistically achievable in the replans for all predicted dose-volumes, excluding D 10 of bladder (P = .03) and rectum (P = .04). Compared with clinical plans, replans showed significant average reductions in D mean for bladder (7.8 Gy; P < .001) and rectum (9.4 Gy; P < .001), while maintaining statistically similar planning target volume, femoral head, and penile bulb dose. KBP dose-volume predictions derived from Pareto plans were more optimal overall than those resulting from manually optimized clinical plans, which significantly improved KBP-assisted plan quality. This work investigates how the plan quality of knowledge databases affects the performance and achievability of dose-volume predictions from a common knowledge-based planning approach for prostate cancer. Bladder and rectum dose-volume predictions derived from a database of standardized Pareto-optimal plans were compared with those derived from clinical plans manually designed by various planners. Dose-volume predictions from the Pareto plan database were significantly lower overall than those from the clinical plan database, without compromising achievability. Copyright © 2018 Elsevier Inc. All rights reserved.

Active in-database processing to support ambient assisted living systems.

PubMed

de Morais, Wagner O; Lundström, Jens; Wickström, Nicholas

2014-08-12

As an alternative to the existing software architectures that underpin the development of smart homes and ambient assisted living (AAL) systems, this work presents a database-centric architecture that takes advantage of active databases and in-database processing. Current platforms supporting AAL systems use database management systems (DBMSs) exclusively for data storage. Active databases employ database triggers to detect and react to events taking place inside or outside of the database. DBMSs can be extended with stored procedures and functions that enable in-database processing. This means that the data processing is integrated and performed within the DBMS. The feasibility and flexibility of the proposed approach were demonstrated with the implementation of three distinct AAL services. The active database was used to detect bed-exits and to discover common room transitions and deviations during the night. In-database machine learning methods were used to model early night behaviors. Consequently, active in-database processing avoids transferring sensitive data outside the database, and this improves performance, security and privacy. Furthermore, centralizing the computation into the DBMS facilitates code reuse, adaptation and maintenance. These are important system properties that take into account the evolving heterogeneity of users, their needs and the devices that are characteristic of smart homes and AAL systems. Therefore, DBMSs can provide capabilities to address requirements for scalability, security, privacy, dependability and personalization in applications of smart environments in healthcare.

Active In-Database Processing to Support Ambient Assisted Living Systems

PubMed Central

de Morais, Wagner O.; Lundström, Jens; Wickström, Nicholas

2014-01-01

As an alternative to the existing software architectures that underpin the development of smart homes and ambient assisted living (AAL) systems, this work presents a database-centric architecture that takes advantage of active databases and in-database processing. Current platforms supporting AAL systems use database management systems (DBMSs) exclusively for data storage. Active databases employ database triggers to detect and react to events taking place inside or outside of the database. DBMSs can be extended with stored procedures and functions that enable in-database processing. This means that the data processing is integrated and performed within the DBMS. The feasibility and flexibility of the proposed approach were demonstrated with the implementation of three distinct AAL services. The active database was used to detect bed-exits and to discover common room transitions and deviations during the night. In-database machine learning methods were used to model early night behaviors. Consequently, active in-database processing avoids transferring sensitive data outside the database, and this improves performance, security and privacy. Furthermore, centralizing the computation into the DBMS facilitates code reuse, adaptation and maintenance. These are important system properties that take into account the evolving heterogeneity of users, their needs and the devices that are characteristic of smart homes and AAL systems. Therefore, DBMSs can provide capabilities to address requirements for scalability, security, privacy, dependability and personalization in applications of smart environments in healthcare. PMID:25120164

Erectile dysfunction is frequent in systemic sclerosis and associated with severe disease: a study of the EULAR Scleroderma Trial and Research group.

PubMed

Foocharoen, Chingching; Tyndall, Alan; Hachulla, Eric; Rosato, Edoardo; Allanore, Yannick; Farge-Bancel, Dominique; Caramaschi, Paola; Airó, Paolo; Nikolaevna, Starovojtova M; Pereira da Silva, José António; Stamenkovic, Bojana; Riemekasten, Gabriela; Rednic, Simona; Sibilia, Jean; Wiland, Piotr; Tarner, Ingo; Smith, Vanessa; Onken, Anna T; Abdel Atty Mohamed, Walid Ahmed; Distler, Oliver; Morović-Vergles, Jadranka; Himsel, Andrea; de la Peña Lefebvre, Paloma Garcia; Hügle, Thomas; Walker, Ulrich A

2012-02-20

Erectile dysfunction (ED) is common in men with systemic sclerosis (SSc) but the demographics, risk factors and treatment coverage for ED are not well known. This study was carried out prospectively in the multinational EULAR Scleroderma Trial and Research database by amending the electronic data-entry system with the International Index of Erectile Function-5 and items related to ED risk factors and treatment. Centres participating in this EULAR Scleroderma Trial and Research substudy were asked to recruit patients consecutively. Of the 130 men studied, only 23 (17.7%) had a normal International Index of Erectile Function-5 score. Thirty-eight per cent of all participants had severe ED (International Index of Erectile Function-5 score ≤ 7). Men with ED were significantly older than subjects without ED (54.8 years vs. 43.3 years, P < 0.001) and more frequently had simultaneous non-SSc-related risk factors such as alcohol consumption. In 82% of SSc patients, the onset of ED was after the manifestation of the first non-Raynaud's symptom (median delay 4.1 years). ED was associated with severe cutaneous, muscular or renal involvement of SSc, elevated pulmonary pressures and restrictive lung disease. ED was treated in only 27.8% of men. The most common treatment was sildenafil, whose efficacy is not established in ED of SSc patients. Severe ED is a common and early problem in men with SSc. Physicians should address modifiable risk factors actively. More research into the pathophysiology, longitudinal development, treatment and psychosocial impact of ED is needed.

Are left ventricular ejection fraction and left atrial diameter related to atrial fibrillation recurrence after catheter ablation?

PubMed Central

Jin, Xiao; Pan, Jianke; Wu, Huanlin; Xu, Danping

2018-01-01

Abstract Atrial fibrillation (AF), the most common form of arrhythmia, is associated with the prevalence of many common cardiovascular and cerebrovascular diseases. Catheter ablation is considered the first-line therapy for AF; however, AF recurrence is very common after catheter ablation. Studies have been performed to analyze the factors associated with AF recurrence, but none have reached a consistent conclusion on whether left ventricular ejection fraction (LVEF) and left atrial diameter (LA diameter) affect AF recurrence after catheter ablation. The databases PubMed, Embase, and the Cochrane Library were used to search for relevant studies up to September 2017. RevMan 5.3.5 software provided by the Cochrane Collaboration Network was used to conduct this meta-analysis. Thirteen studies involving 2825 patients were included in this meta-analysis. Overall, the results revealed that elevated LA diameter values were significantly associated with AF recurrence in patients after catheter ablation (MD = 2.19, 95% CI: 1.63–2.75, P < .001), while baseline LVEF levels were not significantly positively associated with AF recurrence in patients after catheter ablation (MD = −0.91, 95% CI: −1.18 to 1.67, P = .14). Overall, elevated LA diameter may be associated with AF recurrence after catheter ablation; however, there was no direct relationship between LVEF values and AF recurrence after catheter ablation when baseline LVEF values are normal or mildly decreased. Besides, because of publication bias, further studies should be performed to explore the mechanisms underlying AF recurrence. PMID:29768386

Chess databases as a research vehicle in psychology: Modeling large data.

PubMed

Vaci, Nemanja; Bilalić, Merim

2017-08-01

The game of chess has often been used for psychological investigations, particularly in cognitive science. The clear-cut rules and well-defined environment of chess provide a model for investigations of basic cognitive processes, such as perception, memory, and problem solving, while the precise rating system for the measurement of skill has enabled investigations of individual differences and expertise-related effects. In the present study, we focus on another appealing feature of chess-namely, the large archive databases associated with the game. The German national chess database presented in this study represents a fruitful ground for the investigation of multiple longitudinal research questions, since it collects the data of over 130,000 players and spans over 25 years. The German chess database collects the data of all players, including hobby players, and all tournaments played. This results in a rich and complete collection of the skill, age, and activity of the whole population of chess players in Germany. The database therefore complements the commonly used expertise approach in cognitive science by opening up new possibilities for the investigation of multiple factors that underlie expertise and skill acquisition. Since large datasets are not common in psychology, their introduction also raises the question of optimal and efficient statistical analysis. We offer the database for download and illustrate how it can be used by providing concrete examples and a step-by-step tutorial using different statistical analyses on a range of topics, including skill development over the lifetime, birth cohort effects, effects of activity and inactivity on skill, and gender differences.

Differential expression patterns of housekeeping genes increase diagnostic and prognostic value in lung cancer

PubMed Central

Chang, Yu-Chun; Ding, Yan; Dong, Lingsheng; Zhu, Lang-Jing; Jensen, Roderick V.

2018-01-01

Background Using DNA microarrays, we previously identified 451 genes expressed in 19 different human tissues. Although ubiquitously expressed, the variable expression patterns of these “housekeeping genes” (HKGs) could separate one normal human tissue type from another. Current focus on identifying “specific disease markers” is problematic as single gene expression in a given sample represents the specific cellular states of the sample at the time of collection. In this study, we examine the diagnostic and prognostic potential of the variable expressions of HKGs in lung cancers. Methods Microarray and RNA-seq data for normal lungs, lung adenocarcinomas (AD), squamous cell carcinomas of the lung (SQCLC), and small cell carcinomas of the lung (SCLC) were collected from online databases. Using 374 of 451 HKGs, differentially expressed genes between pairs of sample types were determined via two-sided, homoscedastic t-test. Principal component analysis and hierarchical clustering classified normal lung and lung cancers subtypes according to relative gene expression variations. We used uni- and multi-variate cox-regressions to identify significant predictors of overall survival in AD patients. Classifying genes were selected using a set of training samples and then validated using an independent test set. Gene Ontology was examined by PANTHER. Results This study showed that the differential expression patterns of 242, 245, and 99 HKGs were able to distinguish normal lung from AD, SCLC, and SQCLC, respectively. From these, 70 HKGs were common across the three lung cancer subtypes. These HKGs have low expression variation compared to current lung cancer markers (e.g., EGFR, KRAS) and were involved in the most common biological processes (e.g., metabolism, stress response). In addition, the expression pattern of 106 HKGs alone was a significant classifier of AD versus SQCLC. We further highlighted that a panel of 13 HKGs was an independent predictor of overall survival and cumulative risk in AD patients. Discussion Here we report HKG expression patterns may be an effective tool for evaluation of lung cancer states. For example, the differential expression pattern of 70 HKGs alone can separate normal lung tissue from various lung cancers while a panel of 106 HKGs was a capable class predictor of subtypes of non-small cell carcinomas. We also reported that HKGs have significantly lower variance compared to traditional cancer markers across samples, highlighting the robustness of a panel of genes over any one specific biomarker. Using RNA-seq data, we showed that the expression pattern of 13 HKGs is a significant, independent predictor of overall survival for AD patients. This reinforces the predictive power of a HKG panel across different gene expression measurement platforms. Thus, we propose the expression patterns of HKGs alone may be sufficient for the diagnosis and prognosis of individuals with lung cancer. PMID:29761043

Acute sensitivity of freshwater mollusks and commonly tested invertebrates to select chemicals with different toxic models of action

EPA Science Inventory

Previous studies indicate that freshwater mollusks are more sensitive than commonly tested organisms to some chemicals, such as copper and ammonia. Nevertheless, mollusks are generally under-represented in toxicity databases. Studies are needed to generate data with which to comp...

A Search Engine Features Comparison.

ERIC Educational Resources Information Center

Vorndran, Gerald

Until recently, the World Wide Web (WWW) public access search engines have not included many of the advanced commands, options, and features commonly available with the for-profit online database user interfaces, such as DIALOG. This study evaluates the features and characteristics common to both types of search interfaces, examines the Web search…

A particle image velocimetry validation database in the inoor environment using a breathing thermal manakin in rotational motion

EPA Science Inventory

Determination of indoor exposure levels commonly involves assumptions of fully mixed ventilation conditions. In the effort to determine contaminant levels with efficiency, the nodal approach is common in modeling of the indoor environment. To quantify the transport phenomenon or ...

Natural Learning Case Study Archives

ERIC Educational Resources Information Center

Lawler, Robert W.

2015-01-01

Natural Learning Case Study Archives (NLCSA) is a research facility for those interested in using case study analysis to deepen their understanding of common sense knowledge and natural learning (how the mind interacts with everyday experiences to develop common sense knowledge). The database comprises three case study corpora based on experiences…

Open access intrapartum CTG database.

PubMed

Chudáček, Václav; Spilka, Jiří; Burša, Miroslav; Janků, Petr; Hruban, Lukáš; Huptych, Michal; Lhotská, Lenka

2014-01-13

Cardiotocography (CTG) is a monitoring of fetal heart rate and uterine contractions. Since 1960 it is routinely used by obstetricians to assess fetal well-being. Many attempts to introduce methods of automatic signal processing and evaluation have appeared during the last 20 years, however still no significant progress similar to that in the domain of adult heart rate variability, where open access databases are available (e.g. MIT-BIH), is visible. Based on a thorough review of the relevant publications, presented in this paper, the shortcomings of the current state are obvious. A lack of common ground for clinicians and technicians in the field hinders clinically usable progress. Our open access database of digital intrapartum cardiotocographic recordings aims to change that. The intrapartum CTG database consists in total of 552 intrapartum recordings, which were acquired between April 2010 and August 2012 at the obstetrics ward of the University Hospital in Brno, Czech Republic. All recordings were stored in electronic form in the OB TraceVue®;system. The recordings were selected from 9164 intrapartum recordings with clinical as well as technical considerations in mind. All recordings are at most 90 minutes long and start a maximum of 90 minutes before delivery. The time relation of CTG to delivery is known as well as the length of the second stage of labor which does not exceed 30 minutes. The majority of recordings (all but 46 cesarean sections) is - on purpose - from vaginal deliveries. All recordings have available biochemical markers as well as some more general clinical features. Full description of the database and reasoning behind selection of the parameters is presented in the paper. A new open-access CTG database is introduced which should give the research community common ground for comparison of results on reasonably large database. We anticipate that after reading the paper, the reader will understand the context of the field from clinical and technical perspectives which will enable him/her to use the database and also understand its limitations.

Volcanic observation data and simulation database at NIED, Japan (Invited)

NASA Astrophysics Data System (ADS)

Fujita, E.; Ueda, H.; Kozono, T.

2009-12-01

NIED (Nat’l Res. Inst. for Earth Sci. & Disast. Prev.) has a project to develop two volcanic database systems: (1) volcanic observation database; (2) volcanic simulation database. The volcanic observation database is the data archive center obtained by the geophysical observation networks at Mt. Fuji, Miyake, Izu-Oshima, Iwo-jima and Nasu volcanoes, central Japan. The data consist of seismic (both high-sensitivity and broadband), ground deformation (tiltmeter, GPS) and those from other sensors (e.g., rain gauge, gravimeter, magnetometer, pressure gauge.) These data is originally stored in “WIN format,” the Japanese standard format, which is also at the Hi-net (High sensitivity seismic network Japan, http://www.hinet.bosai.go.jp/). NIED joins to WOVOdat and we have prepared to upload our data, via XML format. Our concept of the XML format is 1)a common format for intermediate files to upload into the WOVOdat DB, 2) for data files downloaded from the WOVOdat DB, 3) for data exchanges between observatories without the WOVOdat DB, 4) for common data files in each observatory, 5) for data communications between systems and softwares and 6)a for softwares. NIED is now preparing for (2) the volcanic simulation database. The objective of this project is to support to develop a “real-time” hazard map, i.e., the system which is effective to evaluate volcanic hazard in case of emergency, including the up-to-date conditions. Our system will include lava flow simulation (LavaSIM) and pyroclastic flow simulation (grvcrt). The database will keep many cases of assumed simulations and we can pick up the most probable case as the first evaluation in case the eruption started. The final goals of the both database will realize the volcanic eruption prediction and forecasting in real time by the combination of monitoring data and numerical simulations.

[The 'Beijing clinical database' on severe acute respiratory syndrome patients: its design, process, quality control and evaluation].

PubMed

2004-04-01

To develop a large database on clinical presentation, treatment and prognosis of all clinical diagnosed severe acute respiratory syndrome (SARS) cases in Beijing during the 2003 "crisis", in order to conduct further clinical studies. The database was designed by specialists, under the organization of the Beijing Commanding Center for SARS Treatment and Cure, including 686 data items in six sub-databases: primary medical-care seeking, vital signs, common symptoms and signs, treatment, laboratory and auxiliary test, and cost. All hospitals having received SARS inpatients were involved in the project. Clinical data was transferred and coded by trained doctors and data entry was carried out by trained nurses, according to a uniformed protocol. A series of procedures had been taken before the database was finally established which included programmed logic checking, digit-by-digit check on 5% random sample, data linkage for transferred cases, coding of characterized information, database structure standardization, case reviewe by computer program according to SARS Clinical Diagnosis Criteria issued by the Ministry of Health, and exclusion of unqualified patients. The database involved 2148 probable SARS cases in accordant with the clinical diagnosis criteria, including 1291 with complete records. All cases and record-complete cases showed an almost identical distribution in sex, age, occupation, residence areas and time of onset. The completion rate of data was not significantly different between the two groups except for some items on primary medical-care seeking. Specifically, the data completion rate was 73% - 100% in primary medical-care seeking, 90% in common symptoms and signs, 100% for treatment, 98% for temperature, 90% for pulse, 100% for outcomes and 98% for costs in hospital. The number of cases collected in the Beijing Clinical Database of SARS Patients was fairly complete. Cases with complete records showed that they could serve as excellent representatives of all cases. The completeness of data was quite satisfactory with primary clinical items which allowed for further clinical studies.

Tympanometry in infants: a study of the sensitivity and specificity of 226-Hz and 1,000-Hz probe tones.

PubMed

Carmo, Michele Picanço; Costa, Nayara Thais de Oliveira; Momensohn-Santos, Teresa Maria

2013-10-01

Introduction For infants under 6 months, the literature recommends 1,000-Hz tympanometry, which has a greater sensitivity for the correct identification of middle ear disorders in this population. Objective To systematically analyze national and international publications found in electronic databases that used tympanometry with 226-Hz and 1,000-Hz probe tones. Data Synthesis Initially, we identified 36 articles in the SciELO database, 11 in the Latin American and Caribbean Literature on the Health Sciences (LILACS) database, 199 in MEDLINE, 0 in the Cochrane database, 16 in ISI Web of Knowledge, and 185 in the Scopus database. We excluded 433 articles because they did not fit the selection criteria, leaving 14 publications that were analyzed in their entirety. Conclusions The 1,000-Hz tone test has greater sensitivity and specificity for the correct identification of tympanometric curve changes. However, it is necessary to clarify the doubts that still exist regarding the use of this test frequency. Improved methods for rating curves, standardization of normality criteria, and the types of curves found in infants should be addressed.

Tympanometry in Infants: A Study of the Sensitivity and Specificity of 226-Hz and 1,000-Hz Probe Tones

PubMed Central

Carmo, Michele Picanço; Costa, Nayara Thais de Oliveira; Momensohn-Santos, Teresa Maria

2013-01-01

Introduction For infants under 6 months, the literature recommends 1,000-Hz tympanometry, which has a greater sensitivity for the correct identification of middle ear disorders in this population. Objective To systematically analyze national and international publications found in electronic databases that used tympanometry with 226-Hz and 1,000-Hz probe tones. Data Synthesis Initially, we identified 36 articles in the SciELO database, 11 in the Latin American and Caribbean Literature on the Health Sciences (LILACS) database, 199 in MEDLINE, 0 in the Cochrane database, 16 in ISI Web of Knowledge, and 185 in the Scopus database. We excluded 433 articles because they did not fit the selection criteria, leaving 14 publications that were analyzed in their entirety. Conclusions The 1,000-Hz tone test has greater sensitivity and specificity for the correct identification of tympanometric curve changes. However, it is necessary to clarify the doubts that still exist regarding the use of this test frequency. Improved methods for rating curves, standardization of normality criteria, and the types of curves found in infants should be addressed. PMID:25992044

Multiple Representations-Based Face Sketch-Photo Synthesis.

PubMed

Peng, Chunlei; Gao, Xinbo; Wang, Nannan; Tao, Dacheng; Li, Xuelong; Li, Jie

2016-11-01

Face sketch-photo synthesis plays an important role in law enforcement and digital entertainment. Most of the existing methods only use pixel intensities as the feature. Since face images can be described using features from multiple aspects, this paper presents a novel multiple representations-based face sketch-photo-synthesis method that adaptively combines multiple representations to represent an image patch. In particular, it combines multiple features from face images processed using multiple filters and deploys Markov networks to exploit the interacting relationships between the neighboring image patches. The proposed framework could be solved using an alternating optimization strategy and it normally converges in only five outer iterations in the experiments. Our experimental results on the Chinese University of Hong Kong (CUHK) face sketch database, celebrity photos, CUHK Face Sketch FERET Database, IIIT-D Viewed Sketch Database, and forensic sketches demonstrate the effectiveness of our method for face sketch-photo synthesis. In addition, cross-database and database-dependent style-synthesis evaluations demonstrate the generalizability of this novel method and suggest promising solutions for face identification in forensic science.

A systematic review and meta-analysis of neurological soft signs in relatives of people with schizophrenia

PubMed Central

2011-01-01

Background Neurological soft signs are subtle but observable impairments in motor and sensory functions that are not localized to a specific area of the brain. Neurological soft signs are common in schizophrenia. It has been established that soft signs meet two of five criteria for an endophenotype, namely: association with the illness, and state independence. This review investigated whether soft signs met a further criterion for an endophenotype, namely familial association. It was hypothesized that if familial association were present then neurological soft signs would be: (a) more common in first-degree relatives of people with schizophrenia than in controls; and (b) more common in people with schizophrenia than in their first-degree relatives. Method A systematic search identified potentially eligible studies in the EMBASE (1980-2011), OVID - MEDLINE (1950-2011) and PsycINFO (1806-2011) databases. Studies were included if they carried out a three-way comparison of levels of soft signs between people with schizophrenia, their first-degree relatives, and normal controls. Data were extracted independently by two reviewers and cross-checked by double entry. Results After screening 8678 abstracts, seven studies with 1553 participants were identified. Neurological soft signs were significantly more common in first-degree relatives of people with schizophrenia than in controls (pooled standardised mean difference (SMD) 1.24, 95% confidence interval (c.i) 0.59-1.89). Neurological soft signs were also significantly more common in people with schizophrenia than in their first-degree relatives (SMD 0.92, 95% c.i 0.64-1.20). Sensitivity analyses examining the effects of age and group blinding did not significantly alter the main findings. Conclusions Both hypotheses were confirmed, suggesting that the distribution of neurological soft signs in people with schizophrenia and their first-degree relatives is consistent with the endophenotype criterion of familial association. PMID:21859445

Improving the dictionary lookup approach for disease normalization using enhanced dictionary and query expansion

PubMed Central

Jonnagaddala, Jitendra; Jue, Toni Rose; Chang, Nai-Wen; Dai, Hong-Jie

2016-01-01

The rapidly increasing biomedical literature calls for the need of an automatic approach in the recognition and normalization of disease mentions in order to increase the precision and effectivity of disease based information retrieval. A variety of methods have been proposed to deal with the problem of disease named entity recognition and normalization. Among all the proposed methods, conditional random fields (CRFs) and dictionary lookup method are widely used for named entity recognition and normalization respectively. We herein developed a CRF-based model to allow automated recognition of disease mentions, and studied the effect of various techniques in improving the normalization results based on the dictionary lookup approach. The dataset from the BioCreative V CDR track was used to report the performance of the developed normalization methods and compare with other existing dictionary lookup based normalization methods. The best configuration achieved an F-measure of 0.77 for the disease normalization, which outperformed the best dictionary lookup based baseline method studied in this work by an F-measure of 0.13. Database URL: https://github.com/TCRNBioinformatics/DiseaseExtract PMID:27504009

Databases and coordinated research projects at the IAEA on atomic processes in plasmas

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

Braams, Bastiaan J.; Chung, Hyun-Kyung

2012-05-25

The Atomic and Molecular Data Unit at the IAEA works with a network of national data centres to encourage and coordinate production and dissemination of fundamental data for atomic, molecular and plasma-material interaction (A+M/PMI) processes that are relevant to the realization of fusion energy. The Unit maintains numerical and bibliographical databases and has started a Wiki-style knowledge base. The Unit also contributes to A+M database interface standards and provides a search engine that offers a common interface to multiple numerical A+M/PMI databases. Coordinated Research Projects (CRPs) bring together fusion energy researchers and atomic, molecular and surface physicists for joint workmore » towards the development of new data and new methods. The databases and current CRPs on A+M/PMI processes are briefly described here.« less

FCDD: A Database for Fruit Crops Diseases.

PubMed

Chauhan, Rupal; Jasrai, Yogesh; Pandya, Himanshu; Chaudhari, Suman; Samota, Chand Mal

2014-01-01

Fruit Crops Diseases Database (FCDD) requires a number of biotechnology and bioinformatics tools. The FCDD is a unique bioinformatics resource that compiles information about 162 details on fruit crops diseases, diseases type, its causal organism, images, symptoms and their control. The FCDD contains 171 phytochemicals from 25 fruits, their 2D images and their 20 possible sequences. This information has been manually extracted and manually verified from numerous sources, including other electronic databases, textbooks and scientific journals. FCDD is fully searchable and supports extensive text search. The main focus of the FCDD is on providing possible information of fruit crops diseases, which will help in discovery of potential drugs from one of the common bioresource-fruits. The database was developed using MySQL. The database interface is developed in PHP, HTML and JAVA. FCDD is freely available. http://www.fruitcropsdd.com/

Migration of legacy mumps applications to relational database servers.

PubMed

O'Kane, K C

2001-07-01

An extended implementation of the Mumps language is described that facilitates vendor neutral migration of legacy Mumps applications to SQL-based relational database servers. Implemented as a compiler, this system translates Mumps programs to operating system independent, standard C code for subsequent compilation to fully stand-alone, binary executables. Added built-in functions and support modules extend the native hierarchical Mumps database with access to industry standard, networked, relational database management servers (RDBMS) thus freeing Mumps applications from dependence upon vendor specific, proprietary, unstandardized database models. Unlike Mumps systems that have added captive, proprietary RDMBS access, the programs generated by this development environment can be used with any RDBMS system that supports common network access protocols. Additional features include a built-in web server interface and the ability to interoperate directly with programs and functions written in other languages.

Qualitative Comparison of IGRA and ESRL Radiosonde Archived Databases

NASA Technical Reports Server (NTRS)

Walker, John R.

2014-01-01

Multiple databases of atmospheric profile information are freely available to individuals and groups such as the Natural Environments group. Two of the primary database archives provided by NOAA that are most frequently used are those from the Earth Science Research Laboratory (ESRL) and the Integrated Global Radiosonde Archive (IGRA). Inquiries have been made as to why one database is used as opposed to the other, yet to the best of knowledge, no formal comparison has been performed. The goal of this study is to provide a qualitative comparison of the ESRL and IGRA radiosonde databases. For part of this analyses, 14 upper air observation sites were selected. These sites all have the common attribute of having been used or are planned for use in the development of Range Reference Atmospheres (RRAs) in support of NASA's and DOD's current and future goals.

THE NASA AMES POLYCYCLIC AROMATIC HYDROCARBON INFRARED SPECTROSCOPIC DATABASE: THE COMPUTED SPECTRA

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

Bauschlicher, C. W.; Ricca, A.; Boersma, C.

The astronomical emission features, formerly known as the unidentified infrared bands, are now commonly ascribed to polycyclic aromatic hydrocarbons (PAHs). The laboratory experiments and computational modeling done at the NASA Ames Research Center to create a collection of PAH IR spectra relevant to test and refine the PAH hypothesis have been assembled into a spectroscopic database. This database now contains over 800 PAH spectra spanning 2-2000 {mu}m (5000-5 cm{sup -1}). These data are now available on the World Wide Web at www.astrochem.org/pahdb. This paper presents an overview of the computational spectra in the database and the tools developed to analyzemore » and interpret astronomical spectra using the database. A description of the online and offline user tools available on the Web site is also presented.« less

Environmental Health and Toxicology Resources of the United States National Library of Medicine

PubMed Central

Hochstein, Colette; Arnesen, Stacey; Goshorn, Jeanne

2009-01-01

For over 40 years, the National Library of Medicine’s (NLM) Toxicology and Environmental Health Information Program (TEHIP) has worked to organize and to provide access to an extensive array of environmental health and toxicology resources. During these years, the TEHIP program has evolved from a handful of databases developed primarily for researchers to a broad range of products and services that also serve industry, students, and the general public. TEHIP’s resources include TOXNET® , a collection of databases, including online handbooks, bibliographic references, information on the release of chemicals in the environment, and a chemical dictionary. TEHIP also produces several resources aimed towards the general public, such as the Household Products Database , which helps users explore chemicals often found in common household products, and Tox Town® , an interactive guide to commonly encountered toxic substances, health, and the environment. This paper introduces some of NLM’s environmental health and toxicology resources. PMID:17915629

Conversion of National Health Insurance Service-National Sample Cohort (NHIS-NSC) Database into Observational Medical Outcomes Partnership-Common Data Model (OMOP-CDM).

PubMed

You, Seng Chan; Lee, Seongwon; Cho, Soo-Yeon; Park, Hojun; Jung, Sungjae; Cho, Jaehyeong; Yoon, Dukyong; Park, Rae Woong

2017-01-01

It is increasingly necessary to generate medical evidence applicable to Asian people compared to those in Western countries. Observational Health Data Sciences a Informatics (OHDSI) is an international collaborative which aims to facilitate generating high-quality evidence via creating and applying open-source data analytic solutions to a large network of health databases across countries. We aimed to incorporate Korean nationwide cohort data into the OHDSI network by converting the national sample cohort into Observational Medical Outcomes Partnership-Common Data Model (OMOP-CDM). The data of 1.13 million subjects was converted to OMOP-CDM, resulting in average 99.1% conversion rate. The ACHILLES, open-source OMOP-CDM-based data profiling tool, was conducted on the converted database to visualize data-driven characterization and access the quality of data. The OMOP-CDM version of National Health Insurance Service-National Sample Cohort (NHIS-NSC) can be a valuable tool for multiple aspects of medical research by incorporation into the OHDSI research network.

STRBase: a short tandem repeat DNA database for the human identity testing community

PubMed Central

Ruitberg, Christian M.; Reeder, Dennis J.; Butler, John M.

2001-01-01

The National Institute of Standards and Technology (NIST) has compiled and maintained a Short Tandem Repeat DNA Internet Database (http://www.cstl.nist.gov/biotech/strbase/) since 1997 commonly referred to as STRBase. This database is an information resource for the forensic DNA typing community with details on commonly used short tandem repeat (STR) DNA markers. STRBase consolidates and organizes the abundant literature on this subject to facilitate on-going efforts in DNA typing. Observed alleles and annotated sequence for each STR locus are described along with a review of STR analysis technologies. Additionally, commercially available STR multiplex kits are described, published polymerase chain reaction (PCR) primer sequences are reported, and validation studies conducted by a number of forensic laboratories are listed. To supplement the technical information, addresses for scientists and hyperlinks to organizations working in this area are available, along with the comprehensive reference list of over 1300 publications on STRs used for DNA typing purposes. PMID:11125125

On patterns and re-use in bioinformatics databases.

PubMed

Bell, Michael J; Lord, Phillip

2017-09-01

As the quantity of data being depositing into biological databases continues to increase, it becomes ever more vital to develop methods that enable us to understand this data and ensure that the knowledge is correct. It is widely-held that data percolates between different databases, which causes particular concerns for data correctness; if this percolation occurs, incorrect data in one database may eventually affect many others while, conversely, corrections in one database may fail to percolate to others. In this paper, we test this widely-held belief by directly looking for sentence reuse both within and between databases. Further, we investigate patterns of how sentences are reused over time. Finally, we consider the limitations of this form of analysis and the implications that this may have for bioinformatics database design. We show that reuse of annotation is common within many different databases, and that also there is a detectable level of reuse between databases. In addition, we show that there are patterns of reuse that have previously been shown to be associated with percolation errors. Analytical software is available on request. phillip.lord@newcastle.ac.uk. © The Author(s) 2017. Published by Oxford University Press.

On patterns and re-use in bioinformatics databases

PubMed Central

Bell, Michael J.; Lord, Phillip

2017-01-01

Abstract Motivation: As the quantity of data being depositing into biological databases continues to increase, it becomes ever more vital to develop methods that enable us to understand this data and ensure that the knowledge is correct. It is widely-held that data percolates between different databases, which causes particular concerns for data correctness; if this percolation occurs, incorrect data in one database may eventually affect many others while, conversely, corrections in one database may fail to percolate to others. In this paper, we test this widely-held belief by directly looking for sentence reuse both within and between databases. Further, we investigate patterns of how sentences are reused over time. Finally, we consider the limitations of this form of analysis and the implications that this may have for bioinformatics database design. Results: We show that reuse of annotation is common within many different databases, and that also there is a detectable level of reuse between databases. In addition, we show that there are patterns of reuse that have previously been shown to be associated with percolation errors. Availability and implementation: Analytical software is available on request. Contact: phillip.lord@newcastle.ac.uk PMID:28525546

Reference Clinical Database for Fixation Stability Metrics in Normal Subjects Measured with the MAIA Microperimeter.

PubMed

Morales, Marco U; Saker, Saker; Wilde, Craig; Pellizzari, Carlo; Pallikaris, Aristophanes; Notaroberto, Neil; Rubinstein, Martin; Rui, Chiara; Limoli, Paolo; Smolek, Michael K; Amoaku, Winfried M

2016-11-01

The purpose of this study was to establish a normal reference database for fixation stability measured with the bivariate contour ellipse area (BCEA) in the Macular Integrity Assessment (MAIA) microperimeter. Subjects were 358 healthy volunteers who had the MAIA examination. Fixation stability was assessed using two BCEA fixation indices (63% and 95% proportional values) and the percentage of fixation points within 1° and 2° from the fovea (P1 and P2). Statistical analysis was performed with linear regression and Pearson's product moment correlation coefficient. Average areas of 0.80 deg 2 (min = 0.03, max = 3.90, SD = 0.68) for the index BCEA@63% and 2.40 deg 2 (min = 0.20, max = 11.70, SD = 2.04) for the index BCEA@95% were found. The average values of P1 and P2 were 95% (min = 76, max = 100, SD = 5.31) and 99% (min = 91, max = 100, SD = 1.42), respectively. The Pearson's product moment test showed an almost perfect correlation index, r = 0.999, between BCEA@63% and BCEA@95%. Index P1 showed a very strong correlation with BCEA@63%, r = -0.924, as well as with BCEA@95%, r = -0.925. Index P2 demonstrated a slightly lower correlation with both BCEA@63% and BCEA@95%, r = -0.874 and -0.875, respectively. The single parameter of the BCEA@95% may be taken as accurately reporting fixation stability and serves as a reference database of normal subjects with a cutoff area of 2.40 ± 2.04 deg 2 in MAIA microperimeter. Fixation stability can be measured with different indices. This study originates reference fixation values for the MAIA using a single fixation index.

MicroRNA expression, target genes, and signaling pathways in infants with a ventricular septal defect.

PubMed

Chai, Hui; Yan, Zhaoyuan; Huang, Ke; Jiang, Yuanqing; Zhang, Lin

2018-02-01

This study aimed to systematically investigate the relationship between miRNA expression and the occurrence of ventricular septal defect (VSD), and characterize the miRNA target genes and pathways that can lead to VSD. The miRNAs that were differentially expressed in blood samples from VSD and normal infants were screened and validated by implementing miRNA microarrays and qRT-PCR. The target genes regulated by differentially expressed miRNAs were predicted using three target gene databases. The functions and signaling pathways of the target genes were enriched using the GO database and KEGG database, respectively. The transcription and protein expression of specific target genes in critical pathways were compared in the VSD and normal control groups using qRT-PCR and western blotting, respectively. Compared with the normal control group, the VSD group had 22 differentially expressed miRNAs; 19 were downregulated and three were upregulated. The 10,677 predicted target genes participated in many biological functions related to cardiac development and morphogenesis. Four target genes (mGLUR, Gq, PLC, and PKC) were involved in the PKC pathway and four (ECM, FAK, PI3 K, and PDK1) were involved in the PI3 K-Akt pathway. The transcription and protein expression of these eight target genes were significantly upregulated in the VSD group. The 22 miRNAs that were dysregulated in the VSD group were mainly downregulated, which may result in the dysregulation of several key genes and biological functions related to cardiac development. These effects could also be exerted via the upregulation of eight specific target genes, the subsequent over-activation of the PKC and PI3 K-Akt pathways, and the eventual abnormal cardiac development and VSD.

Is 123I-metaiodobenzylguanidine heart-to-mediastinum ratio dependent on age? From Japanese Society of Nuclear Medicine normal database.

PubMed

Nakajima, Kenichi; Okuda, Koichi; Matsuo, Shinro; Wakabayashi, Hiroshi; Kinuya, Seigo

2018-04-01

Heart-to-mediastinum ratios (HMRs) of 123 I-metaiodobenzylguanidine (MIBG) have usually been applied to prognostic evaluations of heart failure and Lewy body disease. However, whether these ratios depend on patient age has not yet been clarified using normal databases. We analyzed 62 patients (average age 57 ± 19 years, male 45%) derived from a normal database of the Japanese Society of Nuclear Medicine working group. The HMR was calculated from early (15 min) and delayed (3-4 h) anterior planar 123 I-MIBG images. All HMRs were standardized to medium-energy general purpose (MEGP) collimator equivalent conditions using conversion coefficients for the collimator types. Washout rates (WR) were also calculated, and we analyzed whether early and late HMR, and WR are associated with age. Before standardization of HMR to MEGP collimator conditions, HMR and age did not significantly correlate. However, late HMR significantly correlated with age after standardization: late HMR = - 0.0071 × age + 3.69 (r 2  = 0.078, p = 0.028), indicating that a 14-year increase in age corresponded to a decrease in HMR of 0.1. Whereas the lower limit (2.5% quantile) of late HMR was 2.3 for all patients, it was 2.5 and 2.0 for those aged ≤ 63 and > 63 years, respectively. Early HMR tended to be lower in subjects with the higher age (p = 0.076), whereas WR was not affected by age. While late HMR was slightly decreased in elderly patients, the lower limit of 2.2-2.3 can still be used to determine both early and late HMR.

Exploring of the molecular mechanism of rhinitis via bioinformatics methods

PubMed Central

Song, Yufen; Yan, Zhaohui

2018-01-01

The aim of this study was to analyze gene expression profiles for exploring the function and regulatory network of differentially expressed genes (DEGs) in pathogenesis of rhinitis by a bioinformatics method. The gene expression profile of GSE43523 was downloaded from the Gene Expression Omnibus database. The dataset contained 7 seasonal allergic rhinitis samples and 5 non-allergic normal samples. DEGs between rhinitis samples and normal samples were identified via the limma package of R. The webGestal database was used to identify enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of the DEGs. The differentially co-expressed pairs of the DEGs were identified via the DCGL package in R, and the differential co-expression network was constructed based on these pairs. A protein-protein interaction (PPI) network of the DEGs was constructed based on the Search Tool for the Retrieval of Interacting Genes database. A total of 263 DEGs were identified in rhinitis samples compared with normal samples, including 125 downregulated ones and 138 upregulated ones. The DEGs were enriched in 7 KEGG pathways. 308 differential co-expression gene pairs were obtained. A differential co-expression network was constructed, containing 212 nodes. In total, 148 PPI pairs of the DEGs were identified, and a PPI network was constructed based on these pairs. Bioinformatics methods could help us identify significant genes and pathways related to the pathogenesis of rhinitis. Steroid biosynthesis pathway and metabolic pathways might play important roles in the development of allergic rhinitis (AR). Genes such as CDC42 effector protein 5, solute carrier family 39 member A11 and PR/SET domain 10 might be also associated with the pathogenesis of AR, which provided references for the molecular mechanisms of AR. PMID:29257233

A Normalized Direct Approach for Estimating the Parameters of the Normal Ogive Three-Parameter Model for Ability Tests.

ERIC Educational Resources Information Center

Gugel, John F.

A new method for estimating the parameters of the normal ogive three-parameter model for multiple-choice test items--the normalized direct (NDIR) procedure--is examined. The procedure is compared to a more commonly used estimation procedure, Lord's LOGIST, using computer simulations. The NDIR procedure uses the normalized (mid-percentile)…

What Searches Do Users Run on PEDro? An Analysis of 893,971 Search Commands Over a 6-Month Period.

PubMed

Stevens, Matthew L; Moseley, Anne; Elkins, Mark R; Lin, Christine C-W; Maher, Chris G

2016-08-05

Clinicians must be able to search effectively for relevant research if they are to provide evidence-based healthcare. It is therefore relevant to consider how users search databases of evidence in healthcare, including what information users look for and what search strategies they employ. To date such analyses have been restricted to the PubMed database. Although the Physiotherapy Evidence Database (PEDro) is searched millions of times each year, no studies have investigated how users search PEDro. To assess the content and quality of searches conducted on PEDro. Searches conducted on the PEDro website over 6 months were downloaded and the 'get' commands and page-views extracted. The following data were tabulated: the 25 most common searches; the number of search terms used; the frequency of use of simple and advanced searches, including the use of each advanced search field; and the frequency of use of various search strategies. Between August 2014 and January 2015, 893,971 search commands were entered on PEDro. Fewer than 18 % of these searches used the advanced search features of PEDro. 'Musculoskeletal' was the most common subdiscipline searched, while 'low back pain' was the most common individual search. Around 20 % of all searches contained errors. PEDro is a commonly used evidence resource, but searching appears to be sub-optimal in many cases. The effectiveness of searches conducted by users needs to improve, which could be facilitated by methods such as targeted training and amending the search interface.

Bioinformatics approach for choosing the correct reference genes when studying gene expression in human keratinocytes.

PubMed

Beer, Lucian; Mlitz, Veronika; Gschwandtner, Maria; Berger, Tanja; Narzt, Marie-Sophie; Gruber, Florian; Brunner, Patrick M; Tschachler, Erwin; Mildner, Michael

2015-10-01

Reverse transcription polymerase chain reaction (qRT-PCR) has become a mainstay in many areas of skin research. To enable quantitative analysis, it is necessary to analyse expression of reference genes (RGs) for normalization of target gene expression. The selection of reliable RGs therefore has an important impact on the experimental outcome. In this study, we aimed to identify and validate the best suited RGs for qRT-PCR in human primary keratinocytes (KCs) over a broad range of experimental conditions using the novel bioinformatics tool 'RefGenes', which is based on a manually curated database of published microarray data. Expression of 6 RGs identified by RefGenes software and 12 commonly used RGs were validated by qRT-PCR. We assessed whether these 18 markers fulfilled the requirements for a valid RG by the comprehensive ranking of four bioinformatics tools and the coefficient of variation (CV). In an overall ranking, we found GUSB to be the most stably expressed RG, whereas the expression values of the commonly used RGs, GAPDH and B2M were significantly affected by varying experimental conditions. Our results identify RefGenes as a powerful tool for the identification of valid RGs and suggest GUSB as the most reliable RG for KCs. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Blood Phosphorus and Magnesium Levels in 130 Elite Track and Field Athletes

PubMed Central

Malliaropoulos, Nikolaos; Tsitas, Kostas; Porfiriadou, Anthoula; Papalada, Agapi; R.Ames, Paul; Del Buono, Angelo; Lippi, Giuseppe; Maffulli, Nicola

2012-01-01

Purpose This study tested the clinical utility and relevance of serum phosphorus and magnesium as markers possibly useful to monitor training in athletes. Methods Phosphorus and magnesium serum concentrations of 130 elite track and field athletes (65 males and 65 females, age range 20-30 years) from the National Athletics Sports Medicine Center database in Thessaloniki, Greece were measured. Results Abnormal results were found in 61 (47%) athletes (32 men and 29 women). In male athletes, serum phosphate was higher than normal in 18% and decreased in 1.5%, whereas serum magnesium concentration was higher in 26%, and lower in 3%. Regarding female athletes, higher serum phosphate and magnesium levels were detected in 26% and 17% respectively, whereas decreased serum magnesium was found in 3%. The most common alterations were higher serum phosphate (29/61, 47%) and magnesium concentrations (28/61, 46%). Abnormalities of serum phosphorus and magnesium concentrations were detected in almost half of the athletes. Hyperphosphataemia and hypermagnesaemia were the most common abnormalities. Conclusion The reference intervals used for general population cannot be used for athletes. Given the lack of pathological manifestations, the physiopathological significance of these findings is uncertain. Further studies on the interpretation of reported ion concentrations in athletes should take in account the type of sport practiced and also the possible variations during the training and competition season. PMID:23785576

Automatic detection of the breast border and nipple position on digital mammograms using genetic algorithm for asymmetry approach to detection of microcalcifications.

PubMed

Karnan, M; Thangavel, K

2007-07-01

The presence of microcalcifications in breast tissue is one of the most incident signs considered by radiologist for an early diagnosis of breast cancer, which is one of the most common forms of cancer among women. In this paper, the Genetic Algorithm (GA) is proposed for automatic look at commonly prone area the breast border and nipple position to discover the suspicious regions on digital mammograms based on asymmetries between left and right breast image. The basic idea of the asymmetry approach is to scan left and right images are subtracted to extract the suspicious region. The proposed system consists of two steps: First, the mammogram images are enhanced using median filter, normalize the image, at the pectoral muscle region is excluding the border of the mammogram and comparing for both left and right images from the binary image. Further GA is applied to magnify the detected border. The figure of merit is calculated to evaluate whether the detected border is exact or not. And the nipple position is identified using GA. The some comparisons method is adopted for detection of suspected area. Second, using the border points and nipple position as the reference the mammogram images are aligned and subtracted to extract the suspicious region. The algorithms are tested on 114 abnormal digitized mammograms from Mammogram Image Analysis Society database.

Incidence and characteristics of chemical burns.

PubMed

Koh, Dong-Hee; Lee, Sang-Gil; Kim, Hwan-Cheol

2017-05-01

Chemical burns can lead to serious health outcomes. Previous studies about chemical burns have been performed based on burn center data so these studies have provided limited information about the incidence of chemical burns at the national level. The aim of this study was to evaluate the incidence and characteristics of chemical burns using nationwide databases. A cohort representing the Korean population, which was established using a national health insurance database, and a nationwide workers' compensation database were used to evaluate the incidence and characteristics of chemical burns. Characteristics of the affected body region, depth of burns, industry, task, and causative agents were analyzed from two databases. The incidence of chemical burns was calculated according to employment status. The most common regions involving chemical burns with hospital visits were the skin followed by the eyes. For skin lesions, the hands and wrists were the most commonly affected regions. Second degree burns were the most common in terms of depth of skin lesions. The hospital visit incidence was 1.96 per 10,000 person-year in the general population. The compensated chemical burns incidence was 0.17 per 10,000 person-year. Employees and the self-employed showed a significantly increased risk of chemical burns undergoing hospital visits compared to their dependents. Chemical burns on the skin and eyes are almost equally prevalent. The working environment was associated with increased risk of chemical burns. Our results may aid in estimating the size of the problem and prioritizing prevention of chemical burns. Copyright © 2016 Elsevier Ltd and ISBI. All rights reserved.

Identifying Chinese herbal medicine for premenstrual syndrome: implications from a nationwide database

PubMed Central

2014-01-01

Background Premenstrual syndrome (PMS) occurs in women during their reproductive age with a quite negative impact on their daily lives. Women with PMS experience a wide range of physical or psychological symptoms and seek treatment for them. Chinese herb medicine (CHM) is commonly used for PMS and the goal of this study is to investigate the prescription patterns of CHM for PMS by using a nationwide database. Methods Prescriptions of CHM were obtained from two million beneficiaries randomly sampled from the National Health Insurance Research Database, a nationwide database in Taiwan. The ICD-9 code 625.4 was used to identify patients with PMS. Association rule mining and social network analysis were used to explore both the combinations and the core treatments for PMS. Results During 1998-2011, a total of 14,312 CHM prescriptions for PMS were provided. Jia-Wei-Xiao-Yao-San (JWXYS) was the CHM which had the highest prevalence (37.5% of all prescriptions) and also the core of prescription network for PMS. For combination of two CHM, JWXYS with Cyperus rotundus L. was prescribed most frequently, 7.7% of all prescriptions, followed by JWXYS with Leonurus heterophyllus Sweet, 5.9%, and Cyperus rotundus L. with Leonurus heterophyllus Sweet, 5.6%. Conclusions JWXYS-centered CHM combinations were most commonly prescribed for PMS. To the best of our knowledge, this is the first pharmaco-epidemiological study to review CHM treatments for PMS. However, the efficacy and safety of these commonly used CHM were still lacking. The results of this study provide valuable references for further clinical trials and bench studies. PMID:24969368

Big Data Research in Neurosurgery: A Critical Look at this Popular New Study Design.

PubMed

Oravec, Chesney S; Motiwala, Mustafa; Reed, Kevin; Kondziolka, Douglas; Barker, Fred G; Michael, L Madison; Klimo, Paul

2018-05-01

The use of "big data" in neurosurgical research has become increasingly popular. However, using this type of data comes with limitations. This study aimed to shed light on this new approach to clinical research. We compiled a list of commonly used databases that were not specifically created to study neurosurgical procedures, conditions, or diseases. Three North American journals were manually searched for articles published since 2000 utilizing these and other non-neurosurgery-specific databases. A number of data points per article were collected, tallied, and analyzed.A total of 324 articles were identified since 2000 with an exponential increase since 2011 (257/324, 79%). The Journal of Neurosurgery Publishing Group published the greatest total number (n = 200). The National Inpatient Sample was the most commonly used database (n = 136). The average study size was 114 841 subjects (range, 30-4 146 777). The most prevalent topics were vascular (n = 77) and neuro-oncology (n = 66). When categorizing study objective (recognizing that many papers reported more than 1 type of study objective), "Outcomes" was the most common (n = 154). The top 10 institutions by primary or senior author accounted for 45%-50% of all publications. Harvard Medical School was the top institution, using this research technique with 59 representations (31 by primary author and 28 by senior).The increasing use of data from non-neurosurgery-specific databases presents a unique challenge to the interpretation and application of the study conclusions. The limitations of these studies must be more strongly considered in designing and interpreting these studies.

Identifying Chinese herbal medicine for premenstrual syndrome: implications from a nationwide database.

PubMed

Chen, Hsing-Yu; Huang, Ben-Shian; Lin, Yi-Hsuan; Su, Irene H; Yang, Sien-Hung; Chen, Jiun-Liang; Huang, Jen-Wu; Chen, Yu-Chun

2014-06-27

Premenstrual syndrome (PMS) occurs in women during their reproductive age with a quite negative impact on their daily lives. Women with PMS experience a wide range of physical or psychological symptoms and seek treatment for them. Chinese herb medicine (CHM) is commonly used for PMS and the goal of this study is to investigate the prescription patterns of CHM for PMS by using a nationwide database. Prescriptions of CHM were obtained from two million beneficiaries randomly sampled from the National Health Insurance Research Database, a nationwide database in Taiwan. The ICD-9 code 625.4 was used to identify patients with PMS. Association rule mining and social network analysis were used to explore both the combinations and the core treatments for PMS. During 1998-2011, a total of 14,312 CHM prescriptions for PMS were provided. Jia-Wei-Xiao-Yao-San (JWXYS) was the CHM which had the highest prevalence (37.5% of all prescriptions) and also the core of prescription network for PMS. For combination of two CHM, JWXYS with Cyperus rotundus L. was prescribed most frequently, 7.7% of all prescriptions, followed by JWXYS with Leonurus heterophyllus Sweet, 5.9%, and Cyperus rotundus L. with Leonurus heterophyllus Sweet, 5.6%. JWXYS-centered CHM combinations were most commonly prescribed for PMS. To the best of our knowledge, this is the first pharmaco-epidemiological study to review CHM treatments for PMS. However, the efficacy and safety of these commonly used CHM were still lacking. The results of this study provide valuable references for further clinical trials and bench studies.

A Case Study in Software Adaptation

DTIC Science & Technology

2002-01-01

1 A Case Study in Software Adaptation Giuseppe Valetto Telecom Italia Lab Via Reiss Romoli 274 10148, Turin, Italy +39 011 2288788...configuration of the service; monitoring of database connectivity from within the service; monitoring of crashes and shutdowns of IM servers; monitoring of...of the IM server all share a relational database and a common runtime state repository, which make up the backend tier, and allow replicas to

Toward the automated generation of genome-scale metabolic networks in the SEED.

PubMed

DeJongh, Matthew; Formsma, Kevin; Boillot, Paul; Gould, John; Rycenga, Matthew; Best, Aaron

2007-04-26

Current methods for the automated generation of genome-scale metabolic networks focus on genome annotation and preliminary biochemical reaction network assembly, but do not adequately address the process of identifying and filling gaps in the reaction network, and verifying that the network is suitable for systems level analysis. Thus, current methods are only sufficient for generating draft-quality networks, and refinement of the reaction network is still largely a manual, labor-intensive process. We have developed a method for generating genome-scale metabolic networks that produces substantially complete reaction networks, suitable for systems level analysis. Our method partitions the reaction space of central and intermediary metabolism into discrete, interconnected components that can be assembled and verified in isolation from each other, and then integrated and verified at the level of their interconnectivity. We have developed a database of components that are common across organisms, and have created tools for automatically assembling appropriate components for a particular organism based on the metabolic pathways encoded in the organism's genome. This focuses manual efforts on that portion of an organism's metabolism that is not yet represented in the database. We have demonstrated the efficacy of our method by reverse-engineering and automatically regenerating the reaction network from a published genome-scale metabolic model for Staphylococcus aureus. Additionally, we have verified that our method capitalizes on the database of common reaction network components created for S. aureus, by using these components to generate substantially complete reconstructions of the reaction networks from three other published metabolic models (Escherichia coli, Helicobacter pylori, and Lactococcus lactis). We have implemented our tools and database within the SEED, an open-source software environment for comparative genome annotation and analysis. Our method sets the stage for the automated generation of substantially complete metabolic networks for over 400 complete genome sequences currently in the SEED. With each genome that is processed using our tools, the database of common components grows to cover more of the diversity of metabolic pathways. This increases the likelihood that components of reaction networks for subsequently processed genomes can be retrieved from the database, rather than assembled and verified manually.

A Review of Databases Used in Orthopaedic Surgery Research and an Analysis of Database Use in Arthroscopy: The Journal of Arthroscopic and Related Surgery.

PubMed

Weinreb, Jeffrey H; Yoshida, Ryu; Cote, Mark P; O'Sullivan, Michael B; Mazzocca, Augustus D

2017-01-01

The purpose of this study was to evaluate how database use has changed over time in Arthroscopy: The Journal of Arthroscopic and Related Surgery and to inform readers about available databases used in orthopaedic literature. An extensive literature search was conducted to identify databases used in Arthroscopy and other orthopaedic literature. All articles published in Arthroscopy between January 1, 2006, and December 31, 2015, were reviewed. A database was defined as a national, widely available set of individual patient encounters, applicable to multiple patient populations, used in orthopaedic research in a peer-reviewed journal, not restricted by encounter setting or visit duration, and with information available in English. Databases used in Arthroscopy included PearlDiver, the American College of Surgeons National Surgical Quality Improvement Program, the Danish Common Orthopaedic Database, the Swedish National Knee Ligament Register, the Hospital Episodes Statistics database, and the National Inpatient Sample. Database use increased significantly from 4 articles in 2013 to 11 articles in 2015 (P = .012), with no database use between January 1, 2006, and December 31, 2012. Database use increased significantly between January 1, 2006, and December 31, 2015, in Arthroscopy. Level IV, systematic review of Level II through IV studies. Copyright © 2016 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Food Composition Database Format and Structure: A User Focused Approach

PubMed Central

Clancy, Annabel K.; Woods, Kaitlyn; McMahon, Anne; Probst, Yasmine

2015-01-01

This study aimed to investigate the needs of Australian food composition database user’s regarding database format and relate this to the format of databases available globally. Three semi structured synchronous online focus groups (M = 3, F = 11) and n = 6 female key informant interviews were recorded. Beliefs surrounding the use, training, understanding, benefits and limitations of food composition data and databases were explored. Verbatim transcriptions underwent preliminary coding followed by thematic analysis with NVivo qualitative analysis software to extract the final themes. Schematic analysis was applied to the final themes related to database format. Desktop analysis also examined the format of six key globally available databases. 24 dominant themes were established, of which five related to format; database use, food classification, framework, accessibility and availability, and data derivation. Desktop analysis revealed that food classification systems varied considerably between databases. Microsoft Excel was a common file format used in all databases, and available software varied between countries. User’s also recognised that food composition databases format should ideally be designed specifically for the intended use, have a user-friendly food classification system, incorporate accurate data with clear explanation of data derivation and feature user input. However, such databases are limited by data availability and resources. Further exploration of data sharing options should be considered. Furthermore, user’s understanding of food composition data and databases limitations is inherent to the correct application of non-specific databases. Therefore, further exploration of user FCDB training should also be considered. PMID:26554836

Normative Velopharyngeal Data in Infants: Implications for Treatment of Cleft Palate.

PubMed

Schenck, Graham C; Perry, Jamie L; Fang, Xiangming

2016-09-01

Identifying normative data related to velopharyngeal muscles and structures may have clinical significance for infants born with cleft palate, especially as they relate to selection of surgical intervention and postsurgical outcomes. Previous studies suggest that patients whose anatomy postsurgically is dissimilar to that of their normative counterparts are at risk for hypernasal speech. However, studies have not documented what constitutes "normal" anatomy for the clinically relevant population-that is, the infant population. The purpose of this study is to examine a magnetic resonance imaging database (n = 29) related to normative velopharyngeal structures and provide a preliminary comparison to 2 selected patients with repaired cleft palate. Twenty-nine healthy infants between 9 and 23 months of age (mean = 15.2 months) with normal craniofacial and velopharyngeal anatomy were recruited to participate in this study. Normative data were compared to 2 infants with repaired cleft palate between 13 and 15 months of age (mean = 14 months). Quantitative craniometric and velopharyngeal measures from the sagittal and oblique coronal image planes were collected. Variables of interest included: levator muscle, velar, and craniometric measures. Females demonstrated significantly larger intravelar segments compared with males. White infants demonstrated significantly larger levator muscles compared to non-white infants. Infants with repaired cleft palate demonstrated increased overall levator muscle length and levator extravelar length compared with infants with normal velopharyngeal anatomy.Data from the present study provide a normative database for future investigators to utilize as a comparative tool when evaluating infants with normal and abnormal velopharyngeal anatomy.

Analysis of molecular pathways in pancreatic ductal adenocarcinomas with a bioinformatics approach.

PubMed

Wang, Yan; Li, Yan

2015-01-01

Pancreatic ductal adenocarcinoma (PDAC) is a leading cause of cancer death worldwide. Our study aimed to reveal molecular mechanisms. Microarray data of GSE15471 (including 39 matching pairs of pancreatic tumor tissues and patient-matched normal tissues) was downloaded from Gene Expression Omnibus (GEO) database. We identified differentially expressed genes (DEGs) in PDAC tissues compared with normal tissues by limma package in R language. Then GO and KEGG pathway enrichment analyses were conducted with online DAVID. In addition, principal component analysis was performed and a protein-protein interaction network was constructed to study relationships between the DEGs through database STRING. A total of 532 DEGs were identified in the 38 PDAC tissues compared with 33 normal tissues. The results of principal component analysis of the top 20 DEGs could differentiate the PDAC tissues from normal tissues directly. In the PPI network, 8 of the 20 DEGs were all key genes of the collagen family. Additionally, FN1 (fibronectin 1) was also a hub node in the network. The genes of the collagen family as well as FN1 were significantly enriched in complement and coagulation cascades, ECM-receptor interaction and focal adhesion pathways. Our results suggest that genes of collagen family and FN1 may play an important role in PDAC progression. Meanwhile, these DEGs and enriched pathways, such as complement and coagulation cascades, ECM-receptor interaction and focal adhesion may be important molecular mechanisms involved in the development and progression of PDAC.

Modeling Error Distributions of Growth Curve Models through Bayesian Methods

ERIC Educational Resources Information Center

Zhang, Zhiyong

2016-01-01

Growth curve models are widely used in social and behavioral sciences. However, typical growth curve models often assume that the errors are normally distributed although non-normal data may be even more common than normal data. In order to avoid possible statistical inference problems in blindly assuming normality, a general Bayesian framework is…

Incremental Validity of the DSM-5 Section III Personality Disorder Traits With Respect to Psychosocial Impairment.

PubMed

Simms, Leonard J; Calabrese, William R

2016-02-01

Traditional personality disorders (PDs) are associated with significant psychosocial impairment. DSM-5 Section III includes an alternative hybrid personality disorder (PD) classification approach, with both type and trait elements, but relatively little is known about the impairments associated with Section III traits. Our objective was to study the incremental validity of Section III traits--compared to normal-range traits, traditional PD criterion counts, and common psychiatric symptomatology--in predicting psychosocial impairment. To that end, 628 current/recent psychiatric patients completed measures of PD traits, normal-range traits, traditional PD criteria, psychiatric symptomatology, and psychosocial impairments. Hierarchical regressions revealed that Section III PD traits incrementally predicted psychosocial impairment over normal-range personality traits, PD criterion counts, and common psychiatric symptomatology. In contrast, the incremental effects for normal-range traits, PD symptom counts, and common psychiatric symptomatology were substantially smaller than for PD traits. These findings have implications for PD classification and the impairment literature more generally.

FamPlex: a resource for entity recognition and relationship resolution of human protein families and complexes in biomedical text mining.

PubMed

Bachman, John A; Gyori, Benjamin M; Sorger, Peter K

2018-06-28

For automated reading of scientific publications to extract useful information about molecular mechanisms it is critical that genes, proteins and other entities be correctly associated with uniform identifiers, a process known as named entity linking or "grounding." Correct grounding is essential for resolving relationships among mined information, curated interaction databases, and biological datasets. The accuracy of this process is largely dependent on the availability of machine-readable resources associating synonyms and abbreviations commonly found in biomedical literature with uniform identifiers. In a task involving automated reading of ∼215,000 articles using the REACH event extraction software we found that grounding was disproportionately inaccurate for multi-protein families (e.g., "AKT") and complexes with multiple subunits (e.g."NF- κB"). To address this problem we constructed FamPlex, a manually curated resource defining protein families and complexes as they are commonly encountered in biomedical text. In FamPlex the gene-level constituents of families and complexes are defined in a flexible format allowing for multi-level, hierarchical membership. To create FamPlex, text strings corresponding to entities were identified empirically from literature and linked manually to uniform identifiers; these identifiers were also mapped to equivalent entries in multiple related databases. FamPlex also includes curated prefix and suffix patterns that improve named entity recognition and event extraction. Evaluation of REACH extractions on a test corpus of ∼54,000 articles showed that FamPlex significantly increased grounding accuracy for families and complexes (from 15 to 71%). The hierarchical organization of entities in FamPlex also made it possible to integrate otherwise unconnected mechanistic information across families, subfamilies, and individual proteins. Applications of FamPlex to the TRIPS/DRUM reading system and the Biocreative VI Bioentity Normalization Task dataset demonstrated the utility of FamPlex in other settings. FamPlex is an effective resource for improving named entity recognition, grounding, and relationship resolution in automated reading of biomedical text. The content in FamPlex is available in both tabular and Open Biomedical Ontology formats at https://github.com/sorgerlab/famplex under the Creative Commons CC0 license and has been integrated into the TRIPS/DRUM and REACH reading systems.

Analysis of the Astronomy Diagnostic Test

NASA Astrophysics Data System (ADS)

Brogt, Erik; Sabers, Darrell; Prather, Edward E.; Deming, Grace L.; Hufnagel, Beth; Slater, Timothy F.

Seventy undergraduate class sections were examined from the database of Astronomy Diagnostic Test (ADT) results of Deming and Hufnagel to determine if course format correlated with ADT normalized gain scores. Normalized gains were calculated for four different classroom scenarios: lecture, lecture with discussion, lecture with lab, and lecture with both lab and discussion. Statistical analysis shows that there are no significant differences in normalized gain among the self- reported classroom formats. Prerequisites related to mathematics courses did show differences in normalized gain. Of all reported course activities, only the lecture and the readings for the course correlate significantly with the normalized gain. This analysis suggests that the ADT may not have enough sensitivity to measure differences in the effectiveness of different course formats because of the wide range of topics that the ADT addresses with few questions. Different measures of gain and their biases are discussed. We argue that the use of the normalized gain is not always warranted because of its strong bias toward high pretest scores.

filltex: Automatic queries to ADS and INSPIRE databases to fill LaTex bibliography

NASA Astrophysics Data System (ADS)

Gerosa, Davide; Vallisneri, Michele

2017-05-01

filltex is a simple tool to fill LaTex reference lists with records from the ADS and INSPIRE databases. ADS and INSPIRE are the most common databases used among the theoretical physics and astronomy scientific communities, respectively. filltex automatically looks for all citation labels present in a tex document and, by means of web-scraping, downloads all the required citation records from either of the two databases. filltex significantly speeds up the LaTex scientific writing workflow, as all required actions (compile the tex file, fill the bibliography, compile the bibliography, compile the tex file again) are automated in a single command. We also provide an integration of filltex for the macOS LaTex editor TexShop.

Development and validation of a Database Forensic Metamodel (DBFM)

PubMed Central

Al-dhaqm, Arafat; Razak, Shukor; Othman, Siti Hajar; Ngadi, Asri; Ahmed, Mohammed Nazir; Ali Mohammed, Abdulalem

2017-01-01

Database Forensics (DBF) is a widespread area of knowledge. It has many complex features and is well known amongst database investigators and practitioners. Several models and frameworks have been created specifically to allow knowledge-sharing and effective DBF activities. However, these are often narrow in focus and address specified database incident types. We have analysed 60 such models in an attempt to uncover how numerous DBF activities are really public even when the actions vary. We then generate a unified abstract view of DBF in the form of a metamodel. We identified, extracted, and proposed a common concept and reconciled concept definitions to propose a metamodel. We have applied a metamodelling process to guarantee that this metamodel is comprehensive and consistent. PMID:28146585

Reinforcement learning interfaces for biomedical database systems.

PubMed

Rudowsky, I; Kulyba, O; Kunin, M; Parsons, S; Raphan, T

2006-01-01

Studies of neural function that are carried out in different laboratories and that address different questions use a wide range of descriptors for data storage, depending on the laboratory and the individuals that input the data. A common approach to describe non-textual data that are referenced through a relational database is to use metadata descriptors. We have recently designed such a prototype system, but to maintain efficiency and a manageable metadata table, free formatted fields were designed as table entries. The database interface application utilizes an intelligent agent to improve integrity of operation. The purpose of this study was to investigate how reinforcement learning algorithms can assist the user in interacting with the database interface application that has been developed to improve the performance of the system.

Very large database of lipids: rationale and design.

PubMed

Martin, Seth S; Blaha, Michael J; Toth, Peter P; Joshi, Parag H; McEvoy, John W; Ahmed, Haitham M; Elshazly, Mohamed B; Swiger, Kristopher J; Michos, Erin D; Kwiterovich, Peter O; Kulkarni, Krishnaji R; Chimera, Joseph; Cannon, Christopher P; Blumenthal, Roger S; Jones, Steven R

2013-11-01

Blood lipids have major cardiovascular and public health implications. Lipid-lowering drugs are prescribed based in part on categorization of patients into normal or abnormal lipid metabolism, yet relatively little emphasis has been placed on: (1) the accuracy of current lipid measures used in clinical practice, (2) the reliability of current categorizations of dyslipidemia states, and (3) the relationship of advanced lipid characterization to other cardiovascular disease biomarkers. To these ends, we developed the Very Large Database of Lipids (NCT01698489), an ongoing database protocol that harnesses deidentified data from the daily operations of a commercial lipid laboratory. The database includes individuals who were referred for clinical purposes for a Vertical Auto Profile (Atherotech Inc., Birmingham, AL), which directly measures cholesterol concentrations of low-density lipoprotein, very low-density lipoprotein, intermediate-density lipoprotein, high-density lipoprotein, their subclasses, and lipoprotein(a). Individual Very Large Database of Lipids studies, ranging from studies of measurement accuracy, to dyslipidemia categorization, to biomarker associations, to characterization of rare lipid disorders, are investigator-initiated and utilize peer-reviewed statistical analysis plans to address a priori hypotheses/aims. In the first database harvest (Very Large Database of Lipids 1.0) from 2009 to 2011, there were 1 340 614 adult and 10 294 pediatric patients; the adult sample had a median age of 59 years (interquartile range, 49-70 years) with even representation by sex. Lipid distributions closely matched those from the population-representative National Health and Nutrition Examination Survey. The second harvest of the database (Very Large Database of Lipids 2.0) is underway. Overall, the Very Large Database of Lipids database provides an opportunity for collaboration and new knowledge generation through careful examination of granular lipid data on a large scale. © 2013 Wiley Periodicals, Inc.

SNaX: A Database of Supernova X-Ray Light Curves

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

Ross, Mathias; Dwarkadas, Vikram V., E-mail: Mathias_Ross@msn.com, E-mail: vikram@oddjob.uchicago.edu

We present the Supernova X-ray Database (SNaX), a compilation of the X-ray data from young supernovae (SNe). The database includes the X-ray fluxes and luminosities of young SNe, from days to years after outburst. The original goal and intent of this study was to present a database of Type IIn SNe (SNe IIn), which we have accomplished. Our ongoing goal is to expand the database to include all SNe for which published data are available. The database interface allows one to search for SNe using various criteria, plot all or selected data points, and download both the data and themore » plot. The plotting facility allows for significant customization. There is also a facility for the user to submit data that can be directly incorporated into the database. We include an option to fit the decay of any given SN light curve with a power-law. The database includes a conversion of most data points to a common 0.3–8 keV band so that SN light curves may be directly compared with each other. A mailing list has been set up to disseminate information about the database. We outline the structure and function of the database, describe its various features, and outline the plans for future expansion.« less

Frequency and pattern of Chinese herbal medicine prescriptions for urticaria in Taiwan during 2009: analysis of the national health insurance database

PubMed Central

2013-01-01

Background Large-scale pharmaco-epidemiological studies of Chinese herbal medicine (CHM) for treatment of urticaria are few, even though clinical trials showed some CHM are effective. The purpose of this study was to explore the frequencies and patterns of CHM prescriptions for urticaria by analysing the population-based CHM database in Taiwan. Methods This study was linked to and processed through the complete traditional CHM database of the National Health Insurance Research Database in Taiwan during 2009. We calculated the frequencies and patterns of CHM prescriptions used for treatment of urticaria, of which the diagnosis was defined as the single ICD-9 Code of 708. Frequent itemset mining, as applied to data mining, was used to analyse co-prescription of CHM for patients with urticaria. Results There were 37,386 subjects who visited traditional Chinese Medicine clinics for urticaria in Taiwan during 2009 and received a total of 95,765 CHM prescriptions. Subjects between 18 and 35 years of age comprised the largest number of those treated (32.76%). In addition, women used CHM for urticaria more frequently than men (female:male = 1.94:1). There was an average of 5.54 items prescribed in the form of either individual Chinese herbs or a formula in a single CHM prescription for urticaria. Bai-Xian-Pi (Dictamnus dasycarpus Turcz) was the most commonly prescribed single Chinese herb while Xiao-Feng San was the most commonly prescribed Chinese herbal formula. The most commonly prescribed CHM drug combination was Xiao-Feng San plus Bai-Xian-Pi while the most commonly prescribed triple drug combination was Xiao-Feng San, Bai-Xian-Pi, and Di-Fu Zi (Kochia scoparia). Conclusions In view of the popularity of CHM such as Xiao-Feng San prescribed for the wind-heat pattern of urticaria in this study, a large-scale, randomized clinical trial is warranted to research their efficacy and safety. PMID:23947955

Frequency and pattern of Chinese herbal medicine prescriptions for urticaria in Taiwan during 2009: analysis of the national health insurance database.

PubMed

Chien, Pei-Shan; Tseng, Yu-Fang; Hsu, Yao-Chin; Lai, Yu-Kai; Weng, Shih-Feng

2013-08-15

Large-scale pharmaco-epidemiological studies of Chinese herbal medicine (CHM) for treatment of urticaria are few, even though clinical trials showed some CHM are effective. The purpose of this study was to explore the frequencies and patterns of CHM prescriptions for urticaria by analysing the population-based CHM database in Taiwan. This study was linked to and processed through the complete traditional CHM database of the National Health Insurance Research Database in Taiwan during 2009. We calculated the frequencies and patterns of CHM prescriptions used for treatment of urticaria, of which the diagnosis was defined as the single ICD-9 Code of 708. Frequent itemset mining, as applied to data mining, was used to analyse co-prescription of CHM for patients with urticaria. There were 37,386 subjects who visited traditional Chinese Medicine clinics for urticaria in Taiwan during 2009 and received a total of 95,765 CHM prescriptions. Subjects between 18 and 35 years of age comprised the largest number of those treated (32.76%). In addition, women used CHM for urticaria more frequently than men (female:male = 1.94:1). There was an average of 5.54 items prescribed in the form of either individual Chinese herbs or a formula in a single CHM prescription for urticaria. Bai-Xian-Pi (Dictamnus dasycarpus Turcz) was the most commonly prescribed single Chinese herb while Xiao-Feng San was the most commonly prescribed Chinese herbal formula. The most commonly prescribed CHM drug combination was Xiao-Feng San plus Bai-Xian-Pi while the most commonly prescribed triple drug combination was Xiao-Feng San, Bai-Xian-Pi, and Di-Fu Zi (Kochia scoparia). In view of the popularity of CHM such as Xiao-Feng San prescribed for the wind-heat pattern of urticaria in this study, a large-scale, randomized clinical trial is warranted to research their efficacy and safety.

A diagnostic approach in Alzheimer`s disease using three-dimensional stereotactic surface projections of Fluorine-18-FDG PET

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

Minoshima, S.; Frey, K.A.; Koeppe, R.A.

1995-07-01

To improve the diagnostic performance of PET as an aid in evaluating patients suspected of having Alzheimer`s disease, the authors developed a fully automated method which generates comprehensive image presentations and objective diagnostic indices. Fluorine-18-fluorodeoxyglucose PET image sets were collected from 37 patients with probable Alzheimer`s disease (including questionable and mild dementia), 22 normal subjects and 5 patients with cerebrovascular disease. Following stereotactic anatomic standardization, metabolic activity on an individual`s PET image set was extracted to a set of predefined surface pixels (three-dimensional stereotactic surface projection, 3D-SSP), which was used in the subsequent analysis. A normal database was created bymore » averaging extracted datasets of the normal subjects. Patients` datasets were compared individually with the normal database by calculating a Z-score on a pixel-by-pixel basis and were displayed in 3D-SSP views for visual inspections. Diagnostic indices were then generated based on averaged Z-scores for the association cortices. Patterns and severities of metabolic reduction in patients with probable Alzheimer`s disease were seen in the standard 3D-SSP views of extracted raw data and statistical Z-scores. When discriminating patients with probable Alzheimer`s disease from normal subjects, diagnostic indices of the parietal association cortex and unilaterally averaged parietal-temporal-frontal cortex showed sensitivities of 95% and 97%, respectively, with a specificity of 100%. Neither index yielded false-positive results for cerebrovascular disease. 3D-SSP enables quantitative data extraction and reliable localization of metabolic abnormalities by means of stereotactic coordinates. The proposed method is a promising approach for interpreting functional brain PET scans. 45 refs., 5 figs.« less

Common Variants in Mendelian Kidney Disease Genes and Their Association with Renal Function

PubMed Central

Fuchsberger, Christian; Köttgen, Anna; O’Seaghdha, Conall M.; Pattaro, Cristian; de Andrade, Mariza; Chasman, Daniel I.; Teumer, Alexander; Endlich, Karlhans; Olden, Matthias; Chen, Ming-Huei; Tin, Adrienne; Kim, Young J.; Taliun, Daniel; Li, Man; Feitosa, Mary; Gorski, Mathias; Yang, Qiong; Hundertmark, Claudia; Foster, Meredith C.; Glazer, Nicole; Isaacs, Aaron; Rao, Madhumathi; Smith, Albert V.; O’Connell, Jeffrey R.; Struchalin, Maksim; Tanaka, Toshiko; Li, Guo; Hwang, Shih-Jen; Atkinson, Elizabeth J.; Lohman, Kurt; Cornelis, Marilyn C.; Johansson, Åsa; Tönjes, Anke; Dehghan, Abbas; Couraki, Vincent; Holliday, Elizabeth G.; Sorice, Rossella; Kutalik, Zoltan; Lehtimäki, Terho; Esko, Tõnu; Deshmukh, Harshal; Ulivi, Sheila; Chu, Audrey Y.; Murgia, Federico; Trompet, Stella; Imboden, Medea; Kollerits, Barbara; Pistis, Giorgio; Harris, Tamara B.; Launer, Lenore J.; Aspelund, Thor; Eiriksdottir, Gudny; Mitchell, Braxton D.; Boerwinkle, Eric; Schmidt, Helena; Hofer, Edith; Hu, Frank; Demirkan, Ayse; Oostra, Ben A.; Turner, Stephen T.; Ding, Jingzhong; Andrews, Jeanette S.; Freedman, Barry I.; Giulianini, Franco; Koenig, Wolfgang; Illig, Thomas; Döring, Angela; Wichmann, H.-Erich; Zgaga, Lina; Zemunik, Tatijana; Boban, Mladen; Minelli, Cosetta; Wheeler, Heather E.; Igl, Wilmar; Zaboli, Ghazal; Wild, Sarah H.; Wright, Alan F.; Campbell, Harry; Ellinghaus, David; Nöthlings, Ute; Jacobs, Gunnar; Biffar, Reiner; Ernst, Florian; Homuth, Georg; Kroemer, Heyo K.; Nauck, Matthias; Stracke, Sylvia; Völker, Uwe; Völzke, Henry; Kovacs, Peter; Stumvoll, Michael; Mägi, Reedik; Hofman, Albert; Uitterlinden, Andre G.; Rivadeneira, Fernando; Aulchenko, Yurii S.; Polasek, Ozren; Hastie, Nick; Vitart, Veronique; Helmer, Catherine; Wang, Jie Jin; Stengel, Bénédicte; Ruggiero, Daniela; Bergmann, Sven; Kähönen, Mika; Viikari, Jorma; Nikopensius, Tiit; Province, Michael; Colhoun, Helen; Doney, Alex; Robino, Antonietta; Krämer, Bernhard K.; Portas, Laura; Ford, Ian; Buckley, Brendan M.; Adam, Martin; Thun, Gian-Andri; Paulweber, Bernhard; Haun, Margot; Sala, Cinzia; Mitchell, Paul; Ciullo, Marina; Vollenweider, Peter; Raitakari, Olli; Metspalu, Andres; Palmer, Colin; Gasparini, Paolo; Pirastu, Mario; Jukema, J. Wouter; Probst-Hensch, Nicole M.; Kronenberg, Florian; Toniolo, Daniela; Gudnason, Vilmundur; Shuldiner, Alan R.; Coresh, Josef; Schmidt, Reinhold; Ferrucci, Luigi; van Duijn, Cornelia M.; Borecki, Ingrid; Kardia, Sharon L.R.; Liu, Yongmei; Curhan, Gary C.; Rudan, Igor; Gyllensten, Ulf; Wilson, James F.; Franke, Andre; Pramstaller, Peter P.; Rettig, Rainer; Prokopenko, Inga; Witteman, Jacqueline; Hayward, Caroline; Ridker, Paul M.; Bochud, Murielle; Heid, Iris M.; Siscovick, David S.; Fox, Caroline S.; Kao, W. Linda; Böger, Carsten A.

2013-01-01

Many common genetic variants identified by genome-wide association studies for complex traits map to genes previously linked to rare inherited Mendelian disorders. A systematic analysis of common single-nucleotide polymorphisms (SNPs) in genes responsible for Mendelian diseases with kidney phenotypes has not been performed. We thus developed a comprehensive database of genes for Mendelian kidney conditions and evaluated the association between common genetic variants within these genes and kidney function in the general population. Using the Online Mendelian Inheritance in Man database, we identified 731 unique disease entries related to specific renal search terms and confirmed a kidney phenotype in 218 of these entries, corresponding to mutations in 258 genes. We interrogated common SNPs (minor allele frequency >5%) within these genes for association with the estimated GFR in 74,354 European-ancestry participants from the CKDGen Consortium. However, the top four candidate SNPs (rs6433115 at LRP2, rs1050700 at TSC1, rs249942 at PALB2, and rs9827843 at ROBO2) did not achieve significance in a stage 2 meta-analysis performed in 56,246 additional independent individuals, indicating that these common SNPs are not associated with estimated GFR. The effect of less common or rare variants in these genes on kidney function in the general population and disease-specific cohorts requires further research. PMID:24029420

The ergonomic relevance of anthropometrical proportions. Part I: body length measures.

PubMed

Küchmeister, Gerd; Behrenbruch, Kay; Ursula, Pieper; Leyk, Dieter

2009-06-01

Anthropometrical findings about proportions of the human body have a long tradition; most of them, however, are rather theoretical. To improve this situation a pragmatic and applicable definition of proportions, normal as well as deviating, is needed. The purpose of this paper is to set up three proportion types for body length measures: leggy-normal-stocky, and their rate in the population of adults in an industrial society (Germany). Based on queries of an actual anthropometrical database metrical limits for these three types are suggested regarding their influence on the most important body length measures in standing and sitting positions. The number of cases with normal proportions is about 60%, leggy and stocky types both reaching up to 20%. The metrical limits are proposed in order to account for differences between those proportion types which are relevant for ergonomics. When solving complex multidimensional design tasks (e.g. workplaces, vehicle interior design, personal equipment) users of anthropometrical data who do not have the opportunity to work with multivariate databases need supplementary information about the proportions of the human body. For this reason such supplementary information concerning proportions is being given here by physiological anthropologists. The application of the findings presented is exemplified in scenarios of ergonomic relevance.

Beach Books: 2016-2017. What Do Colleges and Universities Want Students to Read outside Class?

ERIC Educational Resources Information Center

Randall, David

2017-01-01

"Beach Books 2016-17," which covers 348 colleges and universities, continues the National Association of Scholars' long-running record of providing the most comprehensive information about colleges and universities that assign common readings to incoming freshmen. Although there are several databases of common reading assignments, Beach…

Predictors of clinical-pathologic stage discrepancy in oral cavity squamous cell carcinoma: A National Cancer Database study.

PubMed

Kılıç, Sarah S; Kılıç, Suat; Crippen, Meghan M; Varughese, Denny; Eloy, Jean Anderson; Baredes, Soly; Mahmoud, Omar M; Park, Richard Chan Woo

2018-04-01

Few studies have examined the frequency and survival implications of clinicopathologic stage discrepancy in oral cavity squamous cell carcinoma (SCC). Oral cavity SCC cases with full pathologic staging information were identified in the National Cancer Database (NCDB). Clinical and pathologic stages were compared. Multivariate logistic regressions were performed to identify factors associated with stage discrepancy. There were 9110 cases identified, of which 67.3% of the cases were stage concordant, 19.9% were upstaged, and 12.8% were downstaged. The N classification discordance (28.5%) was more common than T classification discordance (27.6%). In cases of T classification discordance, downstaging is more common than upstaging (15.4% vs 12.1% of cases), but in cases of N classification discordance, the reverse is true; upstaging is much more common than downstaging (20.1 vs 8.4% of cases). Clinicopathologic stage discrepancy in oral cavity SCC is a common phenomenon that is associated with a number of clinical factors and has survival implications. © 2018 Wiley Periodicals, Inc.

Short read Illumina data for the de novo assembly of a non-model snail species transcriptome (Radix balthica, Basommatophora, Pulmonata), and a comparison of assembler performance

PubMed Central

2011-01-01

Background Until recently, read lengths on the Solexa/Illumina system were too short to reliably assemble transcriptomes without a reference sequence, especially for non-model organisms. However, with read lengths up to 100 nucleotides available in the current version, an assembly without reference genome should be possible. For this study we created an EST data set for the common pond snail Radix balthica by Illumina sequencing of a normalized transcriptome. Performance of three different short read assemblers was compared with respect to: the number of contigs, their length, depth of coverage, their quality in various BLAST searches and the alignment to mitochondrial genes. Results A single sequencing run of a normalized RNA pool resulted in 16,923,850 paired end reads with median read length of 61 bases. The assemblies generated by VELVET, OASES, and SeqMan NGEN differed in the total number of contigs, contig length, the number and quality of gene hits obtained by BLAST searches against various databases, and contig performance in the mt genome comparison. While VELVET produced the highest overall number of contigs, a large fraction of these were of small size (< 200bp), and gave redundant hits in BLAST searches and the mt genome alignment. The best overall contig performance resulted from the NGEN assembly. It produced the second largest number of contigs, which on average were comparable to the OASES contigs but gave the highest number of gene hits in two out of four BLAST searches against different reference databases. A subsequent meta-assembly of the four contig sets resulted in larger contigs, less redundancy and a higher number of BLAST hits. Conclusion Our results document the first de novo transcriptome assembly of a non-model species using Illumina sequencing data. We show that de novo transcriptome assembly using this approach yields results useful for downstream applications, in particular if a meta-assembly of contig sets is used to increase contig quality. These results highlight the ongoing need for improvements in assembly methodology. PMID:21679424

A 15 Mb large paracentric chromosome 21 inversion identified in Czech population through a pair of flanking duplications.

PubMed

Drabova, Jana; Trkova, Marie; Hancarova, Miroslava; Novotna, Drahuse; Hejtmankova, Michaela; Havlovicova, Marketa; Sedlacek, Zdenek

2014-01-01

Inversions are balanced structural chromosome rearrangements, which can influence gene expression and the risk of unbalanced chromosome constitution in offspring. Many examples of inversion polymorphisms exist in human, affecting both heterochromatic regions and euchromatin. We describe a novel, 15 Mb long paracentric inversion, inv(21)(q21.1q22.11), affecting more than a third of human 21q. Despite of its length, the inversion cannot be detected using karyotyping due to similar band patterns on the normal and inverted chromosomes, and is therefore likely to escape attention. Its identification was aided by the repeated observation of the same pair of 150 kb long duplications present in cis on chromosome 21 in three Czech families subjected to microarray analysis. The finding prompted us to hypothesise that this co-occurrence of two remote duplications could be associated with an inversion of the intervening segment, and this speculation turned out to be right. The inversion was confirmed in a series of FISH experiments which also showed that the second copy of each of the duplications was always located at the opposite end of the inversion. The presence of the same pair of duplications in additional individuals reported in public databases indicates that the inversion may also be present in other populations. Three out of the total of about 4000 chromosomes 21 examined in our sample carried the duplications and were inverted, corresponding to carrier frequency of about 1/660. Although the breakpoints affect protein-coding genes, the occurrence of the inversion in normal parents and siblings of our patients and the occurrence of the duplications in unaffected controls in databases indicate that this rare variant is rather non-pathogenic. The inverted segment carried an identical shared haplotype in the three families studied. The haplotypes, however, diverged very rapidly in the flanking regions, possibly pointing to an ancient founder event at the origin of the inversion. The identification of inv(21)(q21.1q22.11) supports the notion that paracentric inversions are the most common form of chromosomal variation and that some of them may still remain undetected.

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

A Remote Registration Based on MIDAS

NASA Astrophysics Data System (ADS)

JIN, Xin

2017-04-01

We often need for software registration to protect the interests of the software developers. This article narrated one kind of software long-distance registration technology. The registration method is: place the registration information in a database table, after the procedure starts in check table registration information, if it has registered then the procedure may the normal operation; Otherwise, the customer must input the sequence number and registers through the network on the long-distance server. If it registers successfully, then records the registration information in the database table. This remote registration method can protect the rights of software developers.

Hydroacoustic forcing function modeling using DNS database

NASA Technical Reports Server (NTRS)

Zawadzki, I.; Gershfield, J. L.; Na, Y.; Wang, M.

1996-01-01

A wall pressure frequency spectrum model (Blake 1971 ) has been evaluated using databases from Direct Numerical Simulations (DNS) of a turbulent boundary layer (Na & Moin 1996). Good agreement is found for moderate to strong adverse pressure gradient flows in the absence of separation. In the separated flow region, the model underpredicts the directly calculated spectra by an order of magnitude. The discrepancy is attributed to the violation of the model assumptions in that part of the flow domain. DNS computed coherence length scales and the normalized wall pressure cross-spectra are compared with experimental data. The DNS results are consistent with experimental observations.

TOPDOM: database of conservatively located domains and motifs in proteins.

PubMed

Varga, Julia; Dobson, László; Tusnády, Gábor E

2016-09-01

The TOPDOM database-originally created as a collection of domains and motifs located consistently on the same side of the membranes in α-helical transmembrane proteins-has been updated and extended by taking into consideration consistently localized domains and motifs in globular proteins, too. By taking advantage of the recently developed CCTOP algorithm to determine the type of a protein and predict topology in case of transmembrane proteins, and by applying a thorough search for domains and motifs as well as utilizing the most up-to-date version of all source databases, we managed to reach a 6-fold increase in the size of the whole database and a 2-fold increase in the number of transmembrane proteins. TOPDOM database is available at http://topdom.enzim.hu The webpage utilizes the common Apache, PHP5 and MySQL software to provide the user interface for accessing and searching the database. The database itself is generated on a high performance computer. tusnady.gabor@ttk.mta.hu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

A new relational database structure and online interface for the HITRAN database

NASA Astrophysics Data System (ADS)

Hill, Christian; Gordon, Iouli E.; Rothman, Laurence S.; Tennyson, Jonathan

2013-11-01

A new format for the HITRAN database is proposed. By storing the line-transition data in a number of linked tables described by a relational database schema, it is possible to overcome the limitations of the existing format, which have become increasingly apparent over the last few years as new and more varied data are being used by radiative-transfer models. Although the database in the new format can be searched using the well-established Structured Query Language (SQL), a web service, HITRANonline, has been deployed to allow users to make most common queries of the database using a graphical user interface in a web page. The advantages of the relational form of the database to ensuring data integrity and consistency are explored, and the compatibility of the online interface with the emerging standards of the Virtual Atomic and Molecular Data Centre (VAMDC) project is discussed. In particular, the ability to access HITRAN data using a standard query language from other websites, command line tools and from within computer programs is described.

Evaluation of relational and NoSQL database architectures to manage genomic annotations.

PubMed

Schulz, Wade L; Nelson, Brent G; Felker, Donn K; Durant, Thomas J S; Torres, Richard

2016-12-01

While the adoption of next generation sequencing has rapidly expanded, the informatics infrastructure used to manage the data generated by this technology has not kept pace. Historically, relational databases have provided much of the framework for data storage and retrieval. Newer technologies based on NoSQL architectures may provide significant advantages in storage and query efficiency, thereby reducing the cost of data management. But their relative advantage when applied to biomedical data sets, such as genetic data, has not been characterized. To this end, we compared the storage, indexing, and query efficiency of a common relational database (MySQL), a document-oriented NoSQL database (MongoDB), and a relational database with NoSQL support (PostgreSQL). When used to store genomic annotations from the dbSNP database, we found the NoSQL architectures to outperform traditional, relational models for speed of data storage, indexing, and query retrieval in nearly every operation. These findings strongly support the use of novel database technologies to improve the efficiency of data management within the biological sciences. Copyright © 2016 Elsevier Inc. All rights reserved.

CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units

PubMed Central

Liu, Yongchao; Maskell, Douglas L; Schmidt, Bertil

2009-01-01

Background The Smith-Waterman algorithm is one of the most widely used tools for searching biological sequence databases due to its high sensitivity. Unfortunately, the Smith-Waterman algorithm is computationally demanding, which is further compounded by the exponential growth of sequence databases. The recent emergence of many-core architectures, and their associated programming interfaces, provides an opportunity to accelerate sequence database searches using commonly available and inexpensive hardware. Findings Our CUDASW++ implementation (benchmarked on a single-GPU NVIDIA GeForce GTX 280 graphics card and a dual-GPU GeForce GTX 295 graphics card) provides a significant performance improvement compared to other publicly available implementations, such as SWPS3, CBESW, SW-CUDA, and NCBI-BLAST. CUDASW++ supports query sequences of length up to 59K and for query sequences ranging in length from 144 to 5,478 in Swiss-Prot release 56.6, the single-GPU version achieves an average performance of 9.509 GCUPS with a lowest performance of 9.039 GCUPS and a highest performance of 9.660 GCUPS, and the dual-GPU version achieves an average performance of 14.484 GCUPS with a lowest performance of 10.660 GCUPS and a highest performance of 16.087 GCUPS. Conclusion CUDASW++ is publicly available open-source software. It provides a significant performance improvement for Smith-Waterman-based protein sequence database searches by fully exploiting the compute capability of commonly used CUDA-enabled low-cost GPUs. PMID:19416548

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing

PubMed Central

Karimi, Ramin; Hajdu, Andras

2016-01-01

Comprehensive effort for low-cost sequencing in the past few years has led to the growth of complete genome databases. In parallel with this effort, a strong need, fast and cost-effective methods and applications have been developed to accelerate sequence analysis. Identification is the very first step of this task. Due to the difficulties, high costs, and computational challenges of alignment-based approaches, an alternative universal identification method is highly required. Like an alignment-free approach, DNA signatures have provided new opportunities for the rapid identification of species. In this paper, we present an effective pipeline HTSFinder (high-throughput signature finder) with a corresponding k-mer generator GkmerG (genome k-mers generator). Using this pipeline, we determine the frequency of k-mers from the available complete genome databases for the detection of extensive DNA signatures in a reasonably short time. Our application can detect both unique and common signatures in the arbitrarily selected target and nontarget databases. Hadoop and MapReduce as parallel and distributed computing tools with commodity hardware are used in this pipeline. This approach brings the power of high-performance computing into the ordinary desktop personal computers for discovering DNA signatures in large databases such as bacterial genome. A considerable number of detected unique and common DNA signatures of the target database bring the opportunities to improve the identification process not only for polymerase chain reaction and microarray assays but also for more complex scenarios such as metagenomics and next-generation sequencing analysis. PMID:26884678

HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing.

PubMed

Karimi, Ramin; Hajdu, Andras

2016-01-01

Comprehensive effort for low-cost sequencing in the past few years has led to the growth of complete genome databases. In parallel with this effort, a strong need, fast and cost-effective methods and applications have been developed to accelerate sequence analysis. Identification is the very first step of this task. Due to the difficulties, high costs, and computational challenges of alignment-based approaches, an alternative universal identification method is highly required. Like an alignment-free approach, DNA signatures have provided new opportunities for the rapid identification of species. In this paper, we present an effective pipeline HTSFinder (high-throughput signature finder) with a corresponding k-mer generator GkmerG (genome k-mers generator). Using this pipeline, we determine the frequency of k-mers from the available complete genome databases for the detection of extensive DNA signatures in a reasonably short time. Our application can detect both unique and common signatures in the arbitrarily selected target and nontarget databases. Hadoop and MapReduce as parallel and distributed computing tools with commodity hardware are used in this pipeline. This approach brings the power of high-performance computing into the ordinary desktop personal computers for discovering DNA signatures in large databases such as bacterial genome. A considerable number of detected unique and common DNA signatures of the target database bring the opportunities to improve the identification process not only for polymerase chain reaction and microarray assays but also for more complex scenarios such as metagenomics and next-generation sequencing analysis.

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

Standardization of XML Database Exchanges and the James Webb Space Telescope Experience

NASA Technical Reports Server (NTRS)

Gal-Edd, Jonathan; Detter, Ryan; Jones, Ron; Fatig, Curtis C.

2007-01-01

Personnel from the National Aeronautics and Space Administration (NASA) James Webb Space Telescope (JWST) Project have been working with various standard communities such the Object Management Group (OMG) and the Consultative Committee for Space Data Systems (CCSDS) to assist in the definition of a common extensible Markup Language (XML) for database exchange format. The CCSDS and OMG standards are intended for the exchange of core command and telemetry information, not for all database information needed to exercise a NASA space mission. The mission-specific database, containing all the information needed for a space mission, is translated from/to the standard using a translator. The standard is meant to provide a system that encompasses 90% of the information needed for command and telemetry processing. This paper will discuss standardization of the XML database exchange format, tools used, and the JWST experience, as well as future work with XML standard groups both commercial and government.

USDA food and nutrient databases provide the infrastructure for food and nutrition research, policy, and practice.

PubMed

Ahuja, Jaspreet K C; Moshfegh, Alanna J; Holden, Joanne M; Harris, Ellen

2013-02-01

The USDA food and nutrient databases provide the basic infrastructure for food and nutrition research, nutrition monitoring, policy, and dietary practice. They have had a long history that goes back to 1892 and are unique, as they are the only databases available in the public domain that perform these functions. There are 4 major food and nutrient databases released by the Beltsville Human Nutrition Research Center (BHNRC), part of the USDA's Agricultural Research Service. These include the USDA National Nutrient Database for Standard Reference, the Dietary Supplement Ingredient Database, the Food and Nutrient Database for Dietary Studies, and the USDA Food Patterns Equivalents Database. The users of the databases are diverse and include federal agencies, the food industry, health professionals, restaurants, software application developers, academia and research organizations, international organizations, and foreign governments, among others. Many of these users have partnered with BHNRC to leverage funds and/or scientific expertise to work toward common goals. The use of the databases has increased tremendously in the past few years, especially the breadth of uses. These new uses of the data are bound to increase with the increased availability of technology and public health emphasis on diet-related measures such as sodium and energy reduction. Hence, continued improvement of the databases is important, so that they can better address these challenges and provide reliable and accurate data.

Journal of Chemical Education: Software.

ERIC Educational Resources Information Center

Journal of Chemical Education, 1989

1989-01-01

Discusses a visual database of information about chemical elements. Uses a single sided 12-inch, 30-minute, CAV-type videodisk. Contains a picture of almost every element in its stable form at room temperature and normal atmospheric pressure. Can be used with the video controller from "KC? Discoverer." (MVL)

Geochronology Database for Central Colorado

USGS Publications Warehouse

Klein, T.L.; Evans, K.V.; deWitt, E.H.

2010-01-01

This database is a compilation of published and some unpublished isotopic and fission track age determinations in central Colorado. The compiled area extends from the southern Wyoming border to the northern New Mexico border and from approximately the longitude of Denver on the east to Gunnison on the west. Data for the tephrochronology of Pleistocene volcanic ash, carbon-14, Pb-alpha, common-lead, and U-Pb determinations on uranium ore minerals have been excluded.

A Methodology for Benchmarking Relational Database Machines,

DTIC Science & Technology

1984-01-01

user benchmarks is to compare the multiple users to the best-case performance The data for each query classification coll and the performance...called a benchmark. The term benchmark originates from the markers used by sur - veyors in establishing common reference points for their measure...formatted databases. In order to further simplify the problem, we restrict our study to those DBMs which support the relational model. A sur - vey

Digital database of channel cross-section surveys, Mount St. Helens, Washington

USGS Publications Warehouse

Mosbrucker, Adam R.; Spicer, Kurt R.; Major, Jon J.; Saunders, Dennis R.; Christianson, Tami S.; Kingsbury, Cole G.

2015-08-06

Stream-channel cross-section survey data are a fundamental component to studies of fluvial geomorphology. Such data provide important parameters required by many open-channel flow models, sediment-transport equations, sediment-budget computations, and flood-hazard assessments. At Mount St. Helens, Washington, the long-term response of channels to the May 18, 1980, eruption, which dramatically altered the hydrogeomorphic regime of several drainages, is documented by an exceptional time series of repeat stream-channel cross-section surveys. More than 300 cross sections, most established shortly following the eruption, represent more than 100 kilometers of surveyed topography. Although selected cross sections have been published previously in print form, we present a comprehensive digital database that includes geospatial and tabular data. Furthermore, survey data are referenced to a common geographic projection and to common datums. Database design, maintenance, and data dissemination are accomplished through a geographic information system (GIS) platform, which integrates survey data acquired with theodolite, total station, and global navigation satellite system (GNSS) instrumentation. Users can interactively perform advanced queries and geospatial time-series analysis. An accuracy assessment provides users the ability to quantify uncertainty within these data. At the time of publication, this project is ongoing. Regular database updates are expected; users are advised to confirm they are using the latest version.

Network meta-analyses could be improved by searching more sources and by involving a librarian.

PubMed

Li, Lun; Tian, Jinhui; Tian, Hongliang; Moher, David; Liang, Fuxiang; Jiang, Tongxiao; Yao, Liang; Yang, Kehu

2014-09-01

Network meta-analyses (NMAs) aim to rank the benefits (or harms) of interventions, based on all available randomized controlled trials. Thus, the identification of relevant data is critical. We assessed the conduct of the literature searches in NMAs. Published NMAs were retrieved by searching electronic bibliographic databases and other sources. Two independent reviewers selected studies and five trained reviewers abstracted data regarding literature searches, in duplicate. Search method details were examined using descriptive statistics. Two hundred forty-nine NMAs were included. Eight used previous systematic reviews to identify primary studies without further searching, and five did not report any literature searches. In the 236 studies that used electronic databases to identify primary studies, the median number of databases was 3 (interquartile range: 3-5). MEDLINE, EMBASE, and Cochrane Central Register of Controlled Trials were the most commonly used databases. The most common supplemental search methods included reference lists of included studies (48%), reference lists of previous systematic reviews (40%), and clinical trial registries (32%). None of these supplemental methods was conducted in more than 50% of the NMAs. Literature searches in NMAs could be improved by searching more sources, and by involving a librarian or information specialist. Copyright © 2014 Elsevier Inc. All rights reserved.

Homemade zipline and playground track ride injuries in children.

PubMed

Leeper, Christine M; McKenna, Christine; Gaines, Barbara A

2017-09-01

Playground track ride and homemade zipline-related injuries are increasingly common in the emergency department, with serious injuries and even deaths reported. Retrospective review of the National Electronic Injury Surveillance System (NEISS) database (2009-2015), followed by review of our academic pediatric trauma center's prospectively-maintained database (2005-2013). We included children ages 0-17years of age with zipline-related injuries. We recorded annual incidence of zipline-related injury, zipline type (homemade or playground), injuries and mechanism. In the NEISS database, 9397 (95%CI 6728-12,065) total zipline-related injuries were reported (45.9% homemade, 54.1% playground). Homemade but not playground injuries increased over time. Common injuries were fracture (49.8%), contusion/laceration (21.2%) and head injury (12.7%). Fall was predominant mechanism (83%). Age 5-9 was most frequently affected (59%). Our center database (n=35, 40% homemade, 1 fatality) revealed characteristics concordant with NEISS data. Head injury was related to fall height>5ft and impact with another structure. Homemade zipline injuries are increasing. Children ages 5-9 are at particular risk and should be carefully supervised. Despite protective surfaces, playground ziplines cause significant head injury, extremity fracture and high rates of hospital admission. Playground surface standards should be reviewed and revised as needed. Prognosis Study, Level III. Copyright © 2017 Elsevier Inc. All rights reserved.

Reversal to normal anatomy after failed gastric bypass: systematic review of indications, techniques, and outcomes.

PubMed

Pucher, Philip H; Lord, Amy C; Sodergren, Mikael H; Ahmed, Ahmed R; Darzi, Ara; Purkayastha, Sanjay

2016-08-01

Roux-en-Y gastric bypass (RYGB) is one of the most common and most effective procedures performed to combat obesity and obesity-related metabolic disease. In a small proportion of patients, however, complications may necessitate the attempted reversal of RYGB to normal anatomy. The indications for this procedure, as well as technique, complication rate, and success in resolving symptoms are not clearly defined. To assess current literature describing outcomes after reversal of RYGB. A systematic search of online databases was conducted. Two independent researchers identified and extracted data for studies describing outcomes after RYGB reversal surgery. Indications, techniques, and outcomes were compared, with results pooled where possible. Eight articles were included in the final data synthesis, incorporating data for 46 patients. Reversal was undertaken due to metabolic, physical, nutritional, or other complications. All successfully underwent RYGB reversal with no reported mortality. Surgical technique varied greatly across the included studies. Postoperative morbidity was high, with 42% suffering complications (56% of which were major). Symptom relief or improvement was achieved in 82% of cases. Reversal of RYGB may be undertaken for a variety of indications after RYGB. Though this may successfully eliminate or improve symptoms in a large proportion of patients, the risk of morbidity is high. Surgery should be undertaken after careful patient selection and in appropriately skilled centers only. Copyright © 2016 American Society for Bariatric Surgery. Published by Elsevier Inc. All rights reserved.

Team X Spacecraft Instrument Database Consolidation

NASA Technical Reports Server (NTRS)

Wallenstein, Kelly A.

2005-01-01

In the past decade, many changes have been made to Team X's process of designing each spacecraft, with the purpose of making the overall procedure more efficient over time. One such improvement is the use of information databases from previous missions, designs, and research. By referring to these databases, members of the design team can locate relevant instrument data and significantly reduce the total time they spend on each design. The files in these databases were stored in several different formats with various levels of accuracy. During the past 2 months, efforts have been made in an attempt to combine and organize these files. The main focus was in the Instruments department, where spacecraft subsystems are designed based on mission measurement requirements. A common database was developed for all instrument parameters using Microsoft Excel to minimize the time and confusion experienced when searching through files stored in several different formats and locations. By making this collection of information more organized, the files within them have become more easily searchable. Additionally, the new Excel database offers the option of importing its contents into a more efficient database management system in the future. This potential for expansion enables the database to grow and acquire more search features as needed.

multiplierz v2.0: A Python-based ecosystem for shared access and analysis of native mass spectrometry data.

PubMed

Alexander, William M; Ficarro, Scott B; Adelmant, Guillaume; Marto, Jarrod A

2017-08-01

The continued evolution of modern mass spectrometry instrumentation and associated methods represents a critical component in efforts to decipher the molecular mechanisms which underlie normal physiology and understand how dysregulation of biological pathways contributes to human disease. The increasing scale of these experiments combined with the technological diversity of mass spectrometers presents several challenges for community-wide data access, analysis, and distribution. Here we detail a redesigned version of multiplierz, our Python software library which leverages our common application programming interface (mzAPI) for analysis and distribution of proteomic data. New features include support for a wider range of native mass spectrometry file types, interfaces to additional database search engines, compatibility with new reporting formats, and high-level tools to perform post-search proteomic analyses. A GUI desktop environment, mzDesktop, provides access to multiplierz functionality through a user friendly interface. multiplierz is available for download from: https://github.com/BlaisProteomics/multiplierz; and mzDesktop is available for download from: https://sourceforge.net/projects/multiplierz/. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fuzzy-C-Means Clustering Based Segmentation and CNN-Classification for Accurate Segmentation of Lung Nodules

PubMed

K, Jalal Deen; R, Ganesan; A, Merline

2017-07-27

Objective: Accurate segmentation of abnormal and healthy lungs is very crucial for a steadfast computer-aided disease diagnostics. Methods: For this purpose a stack of chest CT scans are processed. In this paper, novel methods are proposed for segmentation of the multimodal grayscale lung CT scan. In the conventional methods using Markov–Gibbs Random Field (MGRF) model the required regions of interest (ROI) are identified. Result: The results of proposed FCM and CNN based process are compared with the results obtained from the conventional method using MGRF model. The results illustrate that the proposed method can able to segment the various kinds of complex multimodal medical images precisely. Conclusion: However, in this paper, to obtain an exact boundary of the regions, every empirical dispersion of the image is computed by Fuzzy C-Means Clustering segmentation. A classification process based on the Convolutional Neural Network (CNN) classifier is accomplished to distinguish the normal tissue and the abnormal tissue. The experimental evaluation is done using the Interstitial Lung Disease (ILD) database. Creative Commons Attribution License

Cadastral Map Assembling Using Generalized Hough Transformation

NASA Astrophysics Data System (ADS)

Liu, Fei; Ohyama, Wataru; Wakabayashi, Tetsushi; Kimura, Fumitaka

There are numerous cadastral maps generated by the past land surveying. The raster digitization of these paper maps is in progress. For effective and efficient use of these maps, we have to assemble the set of maps to make them superimposable on other geographic information in a GIS. The problem can be seen as a complex jigsaw puzzle where the pieces are the cadastral sections extracted from the map. We present an automatic solution to this geographic jigsaw puzzle, based on the generalized Hough transformation that detects the longest common boundary between every piece and its neighbors. The experiments have been conducted using the map of Mie Prefecture, Japan and the French cadastral map. The results of the experiments with the French cadastral maps showed that the proposed method, which consists of a flood filling procedure of internal area and detection and normalization of the north arrow direction, is suitable for assembling the cadastral map. The final goal of the process is to integrate every piece of the puzzle into a national geographic reference frame and database.

Paroxysmal atrial fibrillation recognition based on multi-scale Rényi entropy of ECG.

PubMed

Xin, Yi; Zhao, Yizhang; Mu, Yuanhui; Li, Qin; Shi, Caicheng

2017-07-20

Atrial fibrillation (AF) is a common type of arrhythmia disease, which has a high morbidity and can lead to some serious complications. The ability to detect and in turn prevent AF is extremely significant to the patient and clinician. Using ECG to detect AF and develop a robust and effective algorithm is the primary objective of this study. Some studies show that after AF occurs, the regulatory mechanism of vagus nerve and sympathetic nerve will change. Each R-R interval will be absolutely unequal. After studying the physiological mechanism of AF, we will calculate the Rényi entropy of the wavelet coefficients of heart rate variability (HRV) in order to measure the complexity of PAF signals, as well as extract the multi-scale features of paroxysmal atrial fibrillation (PAF). The data used in this study is obtained from MIT-BIH PAF Prediction Challenge Database and the correct rate in classifying PAF patients from normal persons is 92.48%. The results of this experiment proved that AF could be detected by using this method and, in turn, provide opinions for clinical diagnosis.

A Local DCT-II Feature Extraction Approach for Personal Identification Based on Palmprint

NASA Astrophysics Data System (ADS)

Choge, H. Kipsang; Oyama, Tadahiro; Karungaru, Stephen; Tsuge, Satoru; Fukumi, Minoru

Biometric applications based on the palmprint have recently attracted increased attention from various researchers. In this paper, a method is presented that differs from the commonly used global statistical and structural techniques by extracting and using local features instead. The middle palm area is extracted after preprocessing for rotation, position and illumination normalization. The segmented region of interest is then divided into blocks of either 8×8 or 16×16 pixels in size. The type-II Discrete Cosine Transform (DCT) is applied to transform the blocks into DCT space. A subset of coefficients that encode the low to medium frequency components is selected using the JPEG-style zigzag scanning method. Features from each block are subsequently concatenated into a compact feature vector and used in palmprint verification experiments with palmprints from the PolyU Palmprint Database. Results indicate that this approach achieves better results than many conventional transform-based methods, with an excellent recognition accuracy above 99% and an Equal Error Rate (EER) of less than 1.2% in palmprint verification.

Histopathologic changes in punctal stenosis.

PubMed

Port, Alexander D; Chen, Yao-Tseng; Lelli, Gary J

2013-01-01

To describe the pathologic changes in punctal stenosis by reporting the histopathologic findings in a series of punctoplasty specimens. Observational retrospective chart review. Electronic health records of all patients having punctoplasty over a 2-year period at an academic oculoplastic practice were examined. All patients whose records included pathology reports were entered into a database. Twenty-four patients, representing 30 eyes, had pathology records in the electronic health records. Patients were 75% women and had an average age of 65 (19-88) years. Associated conditions included blepharitis (71%), dry eye syndrome, or Meibomian gland dysfunction (63%). Histopathologic examination demonstrated chronic inflammation in 11 eyes (36.7%), fibrosis in 7 eyes (23.3%), chronic inflammation and fibrosis in 4 eyes (13.3%), squamous metaplasia in 3 eyes (10%), normal conjunctival mucosa in 3 eyes (10%), and Actinomyces israelii canaliculitis in 2 eyes (6.7%). Nearly all histopathologic specimens revealed findings consistent with inflammation, fibrosis, or both. These findings provide evidence to support the hypothesis that the many etiologic causes of punctal stenosis are linked by a common pathophysiologic mechanism involving inflammation.

Heart murmur detection based on wavelet transformation and a synergy between artificial neural network and modified neighbor annealing methods.

PubMed

Eslamizadeh, Gholamhossein; Barati, Ramin

2017-05-01

Early recognition of heart disease plays a vital role in saving lives. Heart murmurs are one of the common heart problems. In this study, Artificial Neural Network (ANN) is trained with Modified Neighbor Annealing (MNA) to classify heart cycles into normal and murmur classes. Heart cycles are separated from heart sounds using wavelet transformer. The network inputs are features extracted from individual heart cycles, and two classification outputs. Classification accuracy of the proposed model is compared with five multilayer perceptron trained with Levenberg-Marquardt, Extreme-learning-machine, back-propagation, simulated-annealing, and neighbor-annealing algorithms. It is also compared with a Self-Organizing Map (SOM) ANN. The proposed model is trained and tested using real heart sounds available in the Pascal database to show the applicability of the proposed scheme. Also, a device to record real heart sounds has been developed and used for comparison purposes too. Based on the results of this study, MNA can be used to produce considerable results as a heart cycle classifier. Copyright © 2017 Elsevier B.V. All rights reserved.

Stuttering

PubMed Central

Perez, Hector R.; Stoeckle, James H.

2016-01-01

Abstract Objective To provide an update on the epidemiology, genetics, pathophysiology, diagnosis, and treatment of developmental stuttering. Quality of evidence The MEDLINE and Cochrane databases were searched for past and recent studies on the epidemiology, genetics, pathophysiology, diagnosis, and treatment of developmental stuttering. Most recommendations are based on small studies, limited-quality evidence, or consensus. Main message Stuttering is a speech disorder, common in persons of all ages, that affects normal fluency and time patterning of speech. Stuttering has been associated with differences in brain anatomy, functioning, and dopamine regulation thought to be due to genetic causes. Attention to making a correct diagnosis or referral in children is important because there is growing consensus that early intervention with speech therapy for children who stutter is critical. For adults, stuttering can be associated with substantial psychosocial morbidity including social anxiety and low quality of life. Pharmacologic treatment has received attention in recent years, but clinical evidence is limited. The mainstay of treatment for children and adults remains speech therapy. Conclusion A growing body of research has attempted to uncover the pathophysiology of stuttering. Referral for speech therapy remains the best option for children and adults. PMID:27303004

The Eruption Forecasting Information System: Volcanic Eruption Forecasting Using Databases

NASA Astrophysics Data System (ADS)

Ogburn, S. E.; Harpel, C. J.; Pesicek, J. D.; Wellik, J.

2016-12-01

Forecasting eruptions, including the onset size, duration, location, and impacts, is vital for hazard assessment and risk mitigation. The Eruption Forecasting Information System (EFIS) project is a new initiative of the US Geological Survey-USAID Volcano Disaster Assistance Program (VDAP) and will advance VDAP's ability to forecast the outcome of volcanic unrest. The project supports probability estimation for eruption forecasting by creating databases useful for pattern recognition, identifying monitoring data thresholds beyond which eruptive probabilities increase, and for answering common forecasting questions. A major component of the project is a global relational database, which contains multiple modules designed to aid in the construction of probabilistic event trees and to answer common questions that arise during volcanic crises. The primary module contains chronologies of volcanic unrest. This module allows us to query eruption chronologies, monitoring data, descriptive information, operational data, and eruptive phases alongside other global databases, such as WOVOdat and the Global Volcanism Program. The EFIS database is in the early stages of development and population; thus, this contribution also is a request for feedback from the community. Preliminary data are already benefitting several research areas. For example, VDAP provided a forecast of the likely remaining eruption duration for Sinabung volcano, Indonesia, using global data taken from similar volcanoes in the DomeHaz database module, in combination with local monitoring time-series data. In addition, EFIS seismologists used a beta-statistic test and empirically-derived thresholds to identify distal volcano-tectonic earthquake anomalies preceding Alaska volcanic eruptions during 1990-2015 to retrospectively evaluate Alaska Volcano Observatory eruption precursors. This has identified important considerations for selecting analog volcanoes for global data analysis, such as differences between closed and open system volcanoes.

Sequencing artifacts in the type A influenza databases and attempts to correct them.

PubMed

Suarez, David L; Chester, Nikki; Hatfield, Jason

2014-07-01

There are over 276 000 influenza gene sequences in public databases, with the quality of the sequences determined by the contributor. As part of a high school class project, influenza sequences with possible errors were identified in the public databases based on the size of the gene being longer than expected, with the hypothesis that these sequences would have an error. Students contacted sequence submitters alerting them of the possible sequence issue(s) and requested they the suspect sequence(s) be correct as appropriate. Type A influenza viruses were screened, and gene segments longer than the accepted size were identified for further analysis. Attention was placed on sequences with additional nucleotides upstream or downstream of the highly conserved non-coding ends of the viral segments. A total of 1081 sequences were identified that met this criterion. Three types of errors were commonly observed: non-influenza primer sequence wasn't removed from the sequence; PCR product was cloned and plasmid sequence was included in the sequence; and Taq polymerase added an adenine at the end of the PCR product. Internal insertions of nucleotide sequence were also commonly observed, but in many cases it was unclear if the sequence was correct or actually contained an error. A total of 215 sequences, or 22.8% of the suspect sequences, were corrected in the public databases in the first year of the student project. Unfortunately 138 additional sequences with possible errors were added to the databases in the second year. Additional awareness of the need for data integrity of sequences submitted to public databases is needed to fully reap the benefits of these large data sets. © 2014 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

The Chinchilla Research Resource Database: resource for an otolaryngology disease model

PubMed Central

Shimoyama, Mary; Smith, Jennifer R.; De Pons, Jeff; Tutaj, Marek; Khampang, Pawjai; Hong, Wenzhou; Erbe, Christy B.; Ehrlich, Garth D.; Bakaletz, Lauren O.; Kerschner, Joseph E.

2016-01-01

The long-tailed chinchilla (Chinchilla lanigera) is an established animal model for diseases of the inner and middle ear, among others. In particular, chinchilla is commonly used to study diseases involving viral and bacterial pathogens and polymicrobial infections of the upper respiratory tract and the ear, such as otitis media. The value of the chinchilla as a model for human diseases prompted the sequencing of its genome in 2012 and the more recent development of the Chinchilla Research Resource Database (http://crrd.mcw.edu) to provide investigators with easy access to relevant datasets and software tools to enhance their research. The Chinchilla Research Resource Database contains a complete catalog of genes for chinchilla and, for comparative purposes, human. Chinchilla genes can be viewed in the context of their genomic scaffold positions using the JBrowse genome browser. In contrast to the corresponding records at NCBI, individual gene reports at CRRD include functional annotations for Disease, Gene Ontology (GO) Biological Process, GO Molecular Function, GO Cellular Component and Pathway assigned to chinchilla genes based on annotations from the corresponding human orthologs. Data can be retrieved via keyword and gene-specific searches. Lists of genes with similar functional attributes can be assembled by leveraging the hierarchical structure of the Disease, GO and Pathway vocabularies through the Ontology Search and Browser tool. Such lists can then be further analyzed for commonalities using the Gene Annotator (GA) Tool. All data in the Chinchilla Research Resource Database is freely accessible and downloadable via the CRRD FTP site or using the download functions available in the search and analysis tools. The Chinchilla Research Resource Database is a rich resource for researchers using, or considering the use of, chinchilla as a model for human disease. Database URL: http://crrd.mcw.edu PMID:27173523

Using a capture–recapture method to assess the frequency of adverse drug reactions in a French university hospital

PubMed Central

Lugardon, Stephanie; Desboeuf, Karine; Fernet, Pierre; Montastruc, Jean-Louis; Lapeyre-Mestre, Maryse

2006-01-01

Aims There is evidence that different methods used to identify and quantify adverse drug reactions (ADR) in hospitals are not exhaustive (spontaneous reporting or computerized medical databases). The combination of these different sources of data could improve knowledge about ADR frequency in hospitals. The aim of this study was to estimate the incidence of serious ADRs handled in medical wards of a French university hospital using data from the Programme de Medicalization des Systemes d’Information (PMSI) and spontaneous reports recorded in the French Pharmacovigilance Database. Methods The study period was the first semester of 2001. From PMSI, all hospitalization summaries including an ICD-10th code related to a potential ADR were selected. From the French Pharmacovigilance Database, all serious ADRs which occurred during the study period and were reported by physicians working in the University Hospital were collected. After identification of common cases, the capture–recapture method was applied in order to estimate the real number of ADRs occurring during the first semester of 2001. Results From PMSI, we identified 274 different hospital stays related to an ADR. Out of 241 reports selected from the French Pharmacovigilance Database, we retained 151 ADRs for analysis. Fifty-two ADRs were common in the two databases, giving an estimated number of serious ADRs of 796 [95% confidence interval (CI) 638, 954], corresponding to 2.9% of inpatients (95% CI 2.3, 3.5). Conclusions This study shows the lack of exhaustiveness of ADR reporting whatever the sources of data and underlines the interest of merging data from different databases to identify fully the real impact of ADR in hospitals. PMID:16842398

Development and application of a database of food ingredient fraud and economically motivated adulteration from 1980 to 2010.

PubMed

Moore, Jeffrey C; Spink, John; Lipp, Markus

2012-04-01

Food ingredient fraud and economically motivated adulteration are emerging risks, but a comprehensive compilation of information about known problematic ingredients and detection methods does not currently exist. The objectives of this research were to collect such information from publicly available articles in scholarly journals and general media, organize into a database, and review and analyze the data to identify trends. The results summarized are a database that will be published in the US Pharmacopeial Convention's Food Chemicals Codex, 8th edition, and includes 1305 records, including 1000 records with analytical methods collected from 677 references. Olive oil, milk, honey, and saffron were the most common targets for adulteration reported in scholarly journals, and potentially harmful issues identified include spices diluted with lead chromate and lead tetraoxide, substitution of Chinese star anise with toxic Japanese star anise, and melamine adulteration of high protein content foods. High-performance liquid chromatography and infrared spectroscopy were the most common analytical detection procedures, and chemometrics data analysis was used in a large number of reports. Future expansion of this database will include additional publically available articles published before 1980 and in other languages, as well as data outside the public domain. The authors recommend in-depth analyses of individual incidents. This report describes the development and application of a database of food ingredient fraud issues from publicly available references. The database provides baseline information and data useful to governments, agencies, and individual companies assessing the risks of specific products produced in specific regions as well as products distributed and sold in other regions. In addition, the report describes current analytical technologies for detecting food fraud and identifies trends and developments. © 2012 US Pharmacupia Journal of Food Science © 2012 Institute of Food Technologistsreg;

Thoracolumbar spine fractures in frontal impact crashes.

PubMed

Pintar, Frank A; Yoganandan, Narayan; Maiman, Dennis J; Scarboro, Mark; Rudd, Rodney W

2012-01-01

There is currently no injury assessment for thoracic or lumbar spine fractures in the motor vehicle crash standards throughout the world. Compression-related thoracolumbar fractures are occurring in frontal impacts and yet the mechanism of injury is poorly understood. The objective of this investigation was to characterize these injuries using real world crash data from the US-DOT-NHTSA NASS-CDS and CIREN databases. Thoracic and lumbar AIS vertebral body fracture codes were searched for in the two databases. The NASS database was used to characterize population trends as a function of crash year and vehicle model year. The CIREN database was used to examine a case series in more detail. From the NASS database there were 2000-4000 occupants in frontal impacts with thoracic and lumbar vertebral body fractures per crash year. There was an increasing trend in incidence rate of thoracolumbar fractures in frontal impact crashes as a function of vehicle model year from 1986 to 2008; this was not the case for other crash types. From the CIREN database, the thoracolumbar spine was most commonly fractured at either the T12 or L1 level. Major, burst type fractures occurred predominantly at T12, L1 or L5; wedge fractures were most common at L1. Most CIREN occupants were belted; there were slightly more females involved; they were almost all in bucket seats; impact location occurred approximately half the time on the road and half off the road. The type of object struck also seemed to have some influence on fractured spine level, suggesting that the crash deceleration pulse may be influential in the type of compression vector that migrates up the spinal column. Future biomechanical studies are required to define mechanistically how these fractures are influenced by these many factors.