The Semanticscience Integrated Ontology (SIO) for biomedical research and knowledge discovery

PubMed Central

2014-01-01

The Semanticscience Integrated Ontology (SIO) is an ontology to facilitate biomedical knowledge discovery. SIO features a simple upper level comprised of essential types and relations for the rich description of arbitrary (real, hypothesized, virtual, fictional) objects, processes and their attributes. SIO specifies simple design patterns to describe and associate qualities, capabilities, functions, quantities, and informational entities including textual, geometrical, and mathematical entities, and provides specific extensions in the domains of chemistry, biology, biochemistry, and bioinformatics. SIO provides an ontological foundation for the Bio2RDF linked data for the life sciences project and is used for semantic integration and discovery for SADI-based semantic web services. SIO is freely available to all users under a creative commons by attribution license. See website for further information: http://sio.semanticscience.org. PMID:24602174

A Comparative Analysis of a Generalized Lanchester Equation Model and a Stochastic Computer Simulation Model.

DTIC Science & Technology

1987-03-01

model is one in which words or numerical descriptions are used to represent an entity or process. An example of a symbolic model is a mathematical ...are the third type of model used in modeling combat attrition. Analytical models are symbolic models which use mathematical symbols and equations to...simplicity and the ease of tracing through the mathematical computations. In this section I will discuss some of the shortcoming which have been

Data model and relational database design for the New England Water-Use Data System (NEWUDS)

USGS Publications Warehouse

Tessler, Steven

2001-01-01

The New England Water-Use Data System (NEWUDS) is a database for the storage and retrieval of water-use data. NEWUDS can handle data covering many facets of water use, including (1) tracking various types of water-use activities (withdrawals, returns, transfers, distributions, consumptive-use, wastewater collection, and treatment); (2) the description, classification and location of places and organizations involved in water-use activities; (3) details about measured or estimated volumes of water associated with water-use activities; and (4) information about data sources and water resources associated with water use. In NEWUDS, each water transaction occurs unidirectionally between two site objects, and the sites and conveyances form a water network. The core entities in the NEWUDS model are site, conveyance, transaction/rate, location, and owner. Other important entities include water resources (used for withdrawals and returns), data sources, and aliases. Multiple water-exchange estimates can be stored for individual transactions based on different methods or data sources. Storage of user-defined details is accommodated for several of the main entities. Numerous tables containing classification terms facilitate detailed descriptions of data items and can be used for routine or custom data summarization. NEWUDS handles single-user and aggregate-user water-use data, can be used for large or small water-network projects, and is available as a stand-alone Microsoft? Access database structure. Users can customize and extend the database, link it to other databases, or implement the design in other relational database applications.

Liberal Entity Extraction: Rapid Construction of Fine-Grained Entity Typing Systems.

PubMed

Huang, Lifu; May, Jonathan; Pan, Xiaoman; Ji, Heng; Ren, Xiang; Han, Jiawei; Zhao, Lin; Hendler, James A

2017-03-01

The ability of automatically recognizing and typing entities in natural language without prior knowledge (e.g., predefined entity types) is a major challenge in processing such data. Most existing entity typing systems are limited to certain domains, genres, and languages. In this article, we propose a novel unsupervised entity-typing framework by combining symbolic and distributional semantics. We start from learning three types of representations for each entity mention: general semantic representation, specific context representation, and knowledge representation based on knowledge bases. Then we develop a novel joint hierarchical clustering and linking algorithm to type all mentions using these representations. This framework does not rely on any annotated data, predefined typing schema, or handcrafted features; therefore, it can be quickly adapted to a new domain, genre, and/or language. Experiments on genres (news and discussion forum) show comparable performance with state-of-the-art supervised typing systems trained from a large amount of labeled data. Results on various languages (English, Chinese, Japanese, Hausa, and Yoruba) and domains (general and biomedical) demonstrate the portability of our framework.

Liberal Entity Extraction: Rapid Construction of Fine-Grained Entity Typing Systems

PubMed Central

Huang, Lifu; May, Jonathan; Pan, Xiaoman; Ji, Heng; Ren, Xiang; Han, Jiawei; Zhao, Lin; Hendler, James A.

2017-01-01

Abstract The ability of automatically recognizing and typing entities in natural language without prior knowledge (e.g., predefined entity types) is a major challenge in processing such data. Most existing entity typing systems are limited to certain domains, genres, and languages. In this article, we propose a novel unsupervised entity-typing framework by combining symbolic and distributional semantics. We start from learning three types of representations for each entity mention: general semantic representation, specific context representation, and knowledge representation based on knowledge bases. Then we develop a novel joint hierarchical clustering and linking algorithm to type all mentions using these representations. This framework does not rely on any annotated data, predefined typing schema, or handcrafted features; therefore, it can be quickly adapted to a new domain, genre, and/or language. Experiments on genres (news and discussion forum) show comparable performance with state-of-the-art supervised typing systems trained from a large amount of labeled data. Results on various languages (English, Chinese, Japanese, Hausa, and Yoruba) and domains (general and biomedical) demonstrate the portability of our framework. PMID:28328252

Relatedness-based Multi-Entity Summarization

PubMed Central

Gunaratna, Kalpa; Yazdavar, Amir Hossein; Thirunarayan, Krishnaprasad; Sheth, Amit; Cheng, Gong

2017-01-01

Representing world knowledge in a machine processable format is important as entities and their descriptions have fueled tremendous growth in knowledge-rich information processing platforms, services, and systems. Prominent applications of knowledge graphs include search engines (e.g., Google Search and Microsoft Bing), email clients (e.g., Gmail), and intelligent personal assistants (e.g., Google Now, Amazon Echo, and Apple’s Siri). In this paper, we present an approach that can summarize facts about a collection of entities by analyzing their relatedness in preference to summarizing each entity in isolation. Specifically, we generate informative entity summaries by selecting: (i) inter-entity facts that are similar and (ii) intra-entity facts that are important and diverse. We employ a constrained knapsack problem solving approach to efficiently compute entity summaries. We perform both qualitative and quantitative experiments and demonstrate that our approach yields promising results compared to two other stand-alone state-of-the-art entity summarization approaches. PMID:29051696

The Planetary Data System Web Catalog Interface--Another Use of the Planetary Data System Data Model

NASA Technical Reports Server (NTRS)

Hughes, S.; Bernath, A.

1995-01-01

The Planetary Data System Data Model consists of a set of standardized descriptions of entities within the Planetary Science Community. These can be real entities in the space exploration domain such as spacecraft, instruments, and targets; conceptual entities such as data sets, archive volumes, and data dictionaries; or the archive data products such as individual images, spectrum, series, and qubes.

78 FR 77669 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-24

... Energy Cooperative, TEC Trading, Inc. Description: Triennial Market Power Update of the ODEC Entities.... Description: Arizona Public Service Company's Second Supplement to December 28, 2012 Triennial Market Power... Independent System Operator, Inc. Description: 12-16-2013 Cleco NITSA NOA Succession Filing to be effective 12...

Generative Inferences Based on Learned Relations

ERIC Educational Resources Information Center

Chen, Dawn; Lu, Hongjing; Holyoak, Keith J.

2017-01-01

A key property of relational representations is their "generativity": From partial descriptions of relations between entities, additional inferences can be drawn about other entities. A major theoretical challenge is to demonstrate how the capacity to make generative inferences could arise as a result of learning relations from…

43 CFR 414.3 - Storage and Interstate Release Agreements.

Code of Federal Regulations, 2013 CFR

2013-10-01

...; potential environmental impacts and potential effects on threatened and endangered species; comments from... date certain, the consuming entity will: (i) Notify the storing entity to develop a specific quantity... be consistent with its State's laws. (9) The agreement must include a description of: (i) The actions...

43 CFR 414.3 - Storage and Interstate Release Agreements.

Code of Federal Regulations, 2012 CFR

2012-10-01

...; potential environmental impacts and potential effects on threatened and endangered species; comments from... date certain, the consuming entity will: (i) Notify the storing entity to develop a specific quantity... be consistent with its State's laws. (9) The agreement must include a description of: (i) The actions...

43 CFR 414.3 - Storage and Interstate Release Agreements.

Code of Federal Regulations, 2010 CFR

2010-10-01

...; potential environmental impacts and potential effects on threatened and endangered species; comments from... date certain, the consuming entity will: (i) Notify the storing entity to develop a specific quantity... be consistent with its State's laws. (9) The agreement must include a description of: (i) The actions...

43 CFR 414.3 - Storage and Interstate Release Agreements.

Code of Federal Regulations, 2011 CFR

2011-10-01

...; potential environmental impacts and potential effects on threatened and endangered species; comments from... date certain, the consuming entity will: (i) Notify the storing entity to develop a specific quantity... be consistent with its State's laws. (9) The agreement must include a description of: (i) The actions...

13 CFR 119.11 - What information will be requested in an application under the PRIME program?

Code of Federal Regulations, 2011 CFR

2011-01-01

... applicant's community partnerships and collaborations with state and local entities, and a description of how such partnerships and collaborations are serving microentrepreneurs. (4) A description of the...

Understanding the Nature of Structures in Education: Recent Developments

ERIC Educational Resources Information Center

Van der Walt, Johannes L.

2015-01-01

In this paper the author discusses how 21st century education researchers could and in his opinion, should approach the scientific description of the various entities that they might encounter. The word "entities" in pedagogical context refers to phenomena and structures such as "an education system", "education",…

47 CFR 1.2112 - Ownership disclosure requirements for applications.

Code of Federal Regulations, 2011 CFR

2011-10-01

... applications. (a) Each application to participate in competitive bidding (i.e., short-form application (see 47..., including a complete disclosure of the identity and relationship of those persons or entities directly or...'s principal business and a description of each such entity's relationship to the applicant (e.g...

Systems Biology Graphical Notation: Activity Flow language Level 1 Version 1.2.

PubMed

Mi, Huaiyu; Schreiber, Falk; Moodie, Stuart; Czauderna, Tobias; Demir, Emek; Haw, Robin; Luna, Augustin; Le Novère, Nicolas; Sorokin, Anatoly; Villéger, Alice

2015-09-04

The Systems Biological Graphical Notation (SBGN) is an international community effort for standardized graphical representations of biological pathways and networks. The goal of SBGN is to provide unambiguous pathway and network maps for readers with different scientific backgrounds as well as to support efficient and accurate exchange of biological knowledge between different research communities, industry, and other players in systems biology. Three SBGN languages, Process Description (PD), Entity Relationship (ER) and Activity Flow (AF), allow for the representation of different aspects of biological and biochemical systems at different levels of detail. The SBGN Activity Flow language represents the influences of activities among various entities within a network. Unlike SBGN PD and ER that focus on the entities and their relationships with others, SBGN AF puts the emphasis on the functions (or activities) performed by the entities, and their effects to the functions of the same or other entities. The nodes (elements) describe the biological activities of the entities, such as protein kinase activity, binding activity or receptor activity, which can be easily mapped to Gene Ontology molecular function terms. The edges (connections) provide descriptions of relationships (or influences) between the activities, e.g., positive influence and negative influence. Among all three languages of SBGN, AF is the closest to signaling pathways in biological literature and textbooks, but its well-defined semantics offer a superior precision in expressing biological knowledge.

Early descriptions of acromegaly and gigantism and their historical evolution as clinical entities.

PubMed

Mammis, Antonios; Eloy, Jean Anderson; Liu, James K

2010-10-01

Giants have been a subject of fascination throughout history. Whereas descriptions of giants have existed in the lay literature for millennia, the first attempt at a medical description was published by Johannes Wier in 1567. However, it was Pierre Marie, in 1886, who established the term "acromegaly" for the first time and established a distinct clinical diagnosis with clear clinical descriptions in 2 patients with the characteristic presentation. Multiple autopsy findings revealed a consistent correlation between acromegaly and pituitary enlargement. In 1909, Harvey Cushing postulated a “hormone of growth" as the underlying pathophysiological trigger involved in pituitary hypersecretion in patients with acromegaly. This theory was supported by his observations of clinical remission in patients with acromegaly in whom he had performed hypophysectomy. In this paper, the authors present some of the early accounts of acromegaly and gigantism, and describe its historical evolution as a medical and surgical entity.

What Is FRBR? A Conceptual Model for the Bibliographic Universe

ERIC Educational Resources Information Center

Tillett, Barbara

2005-01-01

From 1992 to 1995 the IFLA Study Group on Functional Requirements for Bibliographic Records (FRBR) developed an entity relationship model as a generalised view of the bibliographic universe, intended to be independent of any cataloguing code or implementation. The FRBR report itself includes a description of the conceptual model (the entities,…

Multiple or familial café-au-lait spots is neurofibromatosis type 6: clarification of a diagnosis.

PubMed

Madson, Justin G

2012-05-15

A café-au-lait macule (CALM) is an evenly pigmented macule or patch of variable size. Solitary CALMs are common birthmarks in up to 2.5 percent of normal neonates and their incidence rises to up to 25 percent in preschool-aged children. Two or more CALMs occur much less frequently. Multiple lesions may warrant investigation to identify an underlying disease including neurofibromatosis types 1 (NF1), neurofibromatosis type 2, McCune-Albright syndrome, and neurofibromatosis type 1-like syndrome. Considered a hallmark and diagnostic criteria for NF1 is the presence of 6 or more CALMs greater than 0.5 cm in prepubertal individuals. Rare reports describe families which demonstrate the phenomenon of multiple CALMs without other stigmata of NF1 or evidence of other systemic disease. Herein is a description of the condition and justification for this entity to be named Neurofibromatosis type 6.

Data model and relational database design for the New Jersey Water-Transfer Data System (NJWaTr)

USGS Publications Warehouse

Tessler, Steven

2003-01-01

The New Jersey Water-Transfer Data System (NJWaTr) is a database design for the storage and retrieval of water-use data. NJWaTr can manage data encompassing many facets of water use, including (1) the tracking of various types of water-use activities (withdrawals, returns, transfers, distributions, consumptive-use, wastewater collection, and treatment); (2) the storage of descriptions, classifications and locations of places and organizations involved in water-use activities; (3) the storage of details about measured or estimated volumes of water associated with water-use activities; and (4) the storage of information about data sources and water resources associated with water use. In NJWaTr, each water transfer occurs unidirectionally between two site objects, and the sites and conveyances form a water network. The core entities in the NJWaTr model are site, conveyance, transfer/volume, location, and owner. Other important entities include water resource (used for withdrawals and returns), data source, permit, and alias. Multiple water-exchange estimates based on different methods or data sources can be stored for individual transfers. Storage of user-defined details is accommodated for several of the main entities. Many tables contain classification terms to facilitate the detailed description of data items and can be used for routine or custom data summarization. NJWaTr accommodates single-user and aggregate-user water-use data, can be used for large or small water-network projects, and is available as a stand-alone Microsoft? Access database. Data stored in the NJWaTr structure can be retrieved in user-defined combinations to serve visualization and analytical applications. Users can customize and extend the database, link it to other databases, or implement the design in other relational database applications.

15 CFR Supplement No. 8 to Part 748 - Information Required in Requests for Validated End-User (Veu) Authorization

Code of Federal Regulations, 2010 CFR

2010-01-01

... overview of any business activity or corporate relationship that the entity has with either government or... structure, ownership and business of the prospective validated end-user. Include a description of the entity...-site reviews by U.S. Government officials to verify the end-user's compliance with the conditions of...

Automating generation of textual class definitions from OWL to English.

PubMed

Stevens, Robert; Malone, James; Williams, Sandra; Power, Richard; Third, Allan

2011-05-17

Text definitions for entities within bio-ontologies are a cornerstone of the effort to gain a consensus in understanding and usage of those ontologies. Writing these definitions is, however, a considerable effort and there is often a lag between specification of the main part of an ontology (logical descriptions and definitions of entities) and the development of the text-based definitions. The goal of natural language generation (NLG) from ontologies is to take the logical description of entities and generate fluent natural language. The application described here uses NLG to automatically provide text-based definitions from an ontology that has logical descriptions of its entities, so avoiding the bottleneck of authoring these definitions by hand. To produce the descriptions, the program collects all the axioms relating to a given entity, groups them according to common structure, realises each group through an English sentence, and assembles the resulting sentences into a paragraph, to form as 'coherent' a text as possible without human intervention. Sentence generation is accomplished using a generic grammar based on logical patterns in OWL, together with a lexicon for realising atomic entities. We have tested our output for the Experimental Factor Ontology (EFO) using a simple survey strategy to explore the fluency of the generated text and how well it conveys the underlying axiomatisation. Two rounds of survey and improvement show that overall the generated English definitions are found to convey the intended meaning of the axiomatisation in a satisfactory manner. The surveys also suggested that one form of generated English will not be universally liked; that intrusion of too much 'formal ontology' was not liked; and that too much explicit exposure of OWL semantics was also not liked. Our prototype tools can generate reasonable paragraphs of English text that can act as definitions. The definitions were found acceptable by our survey and, as a result, the developers of EFO are sufficiently satisfied with the output that the generated definitions have been incorporated into EFO. Whilst not a substitute for hand-written textual definitions, our generated definitions are a useful starting point. An on-line version of the NLG text definition tool can be found at http://swat.open.ac.uk/tools/. The questionaire and sample generated text definitions may be found at http://mcs.open.ac.uk/nlg/SWAT/bio-ontologies.html.

Automating generation of textual class definitions from OWL to English

PubMed Central

2011-01-01

Background Text definitions for entities within bio-ontologies are a cornerstone of the effort to gain a consensus in understanding and usage of those ontologies. Writing these definitions is, however, a considerable effort and there is often a lag between specification of the main part of an ontology (logical descriptions and definitions of entities) and the development of the text-based definitions. The goal of natural language generation (NLG) from ontologies is to take the logical description of entities and generate fluent natural language. The application described here uses NLG to automatically provide text-based definitions from an ontology that has logical descriptions of its entities, so avoiding the bottleneck of authoring these definitions by hand. Results To produce the descriptions, the program collects all the axioms relating to a given entity, groups them according to common structure, realises each group through an English sentence, and assembles the resulting sentences into a paragraph, to form as ‘coherent’ a text as possible without human intervention. Sentence generation is accomplished using a generic grammar based on logical patterns in OWL, together with a lexicon for realising atomic entities. We have tested our output for the Experimental Factor Ontology (EFO) using a simple survey strategy to explore the fluency of the generated text and how well it conveys the underlying axiomatisation. Two rounds of survey and improvement show that overall the generated English definitions are found to convey the intended meaning of the axiomatisation in a satisfactory manner. The surveys also suggested that one form of generated English will not be universally liked; that intrusion of too much ‘formal ontology’ was not liked; and that too much explicit exposure of OWL semantics was also not liked. Conclusions Our prototype tools can generate reasonable paragraphs of English text that can act as definitions. The definitions were found acceptable by our survey and, as a result, the developers of EFO are sufficiently satisfied with the output that the generated definitions have been incorporated into EFO. Whilst not a substitute for hand-written textual definitions, our generated definitions are a useful starting point. Availability An on-line version of the NLG text definition tool can be found at http://swat.open.ac.uk/tools/. The questionaire and sample generated text definitions may be found at http://mcs.open.ac.uk/nlg/SWAT/bio-ontologies.html. PMID:21624160

Right fusiform response patterns reflect visual object identity rather than semantic similarity.

PubMed

Bruffaerts, Rose; Dupont, Patrick; De Grauwe, Sophie; Peeters, Ronald; De Deyne, Simon; Storms, Gerrit; Vandenberghe, Rik

2013-12-01

We previously reported the neuropsychological consequences of a lesion confined to the middle and posterior part of the right fusiform gyrus (case JA) causing a partial loss of knowledge of visual attributes of concrete entities in the absence of category-selectivity (animate versus inanimate). We interpreted this in the context of a two-step model that distinguishes structural description knowledge from associative-semantic processing and implicated the lesioned area in the former process. To test this hypothesis in the intact brain, multi-voxel pattern analysis was used in a series of event-related fMRI studies in a total of 46 healthy subjects. We predicted that activity patterns in this region would be determined by the identity of rather than the conceptual similarity between concrete entities. In a prior behavioral experiment features were generated for each entity by more than 1000 subjects. Based on a hierarchical clustering analysis the entities were organised into 3 semantic clusters (musical instruments, vehicles, tools). Entities were presented as words or pictures. With foveal presentation of pictures, cosine similarity between fMRI response patterns in right fusiform cortex appeared to reflect both the identity of and the semantic similarity between the entities. No such effects were found for words in this region. The effect of object identity was invariant for location, scaling, orientation axis and color (grayscale versus color). It also persisted for different exemplars referring to a same concrete entity. The apparent semantic similarity effect however was not invariant. This study provides further support for a neurobiological distinction between structural description knowledge and processing of semantic relationships and confirms the role of right mid-posterior fusiform cortex in the former process, in accordance with previous lesion evidence. © 2013.

7 CFR 1738.16 - Eligible entities.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 11 2010-01-01 2010-01-01 false Eligible entities. 1738.16 Section 1738.16... Eligible entities. (a) RUS makes broadband loans to legally organized entities providing, or proposing to provide, broadband services in eligible rural communities. (1) Types of eligible entities include...

7 CFR 1738.16 - Eligible entities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 11 2011-01-01 2011-01-01 false Eligible entities. 1738.16 Section 1738.16... Eligible entities. (a) RUS makes broadband loans to legally organized entities providing, or proposing to provide, broadband services in eligible rural communities. (1) Types of eligible entities include...

42 CFR 456.712 - Annual report.

Code of Federal Regulations, 2013 CFR

2013-10-01

... program. (2) A description of how pharmacies performing prospective DUR without computers are expected to...) A description of the steps taken by the State Agency to monitor compliance by pharmacies with the... entities such as the Medicaid Fraud Control Unit and State Board of Pharmacy. The annual report also must...

42 CFR 456.712 - Annual report.

Code of Federal Regulations, 2014 CFR

2014-10-01

... program. (2) A description of how pharmacies performing prospective DUR without computers are expected to...) A description of the steps taken by the State Agency to monitor compliance by pharmacies with the... entities such as the Medicaid Fraud Control Unit and State Board of Pharmacy. The annual report also must...

42 CFR 456.712 - Annual report.

Code of Federal Regulations, 2010 CFR

2010-10-01

... program. (2) A description of how pharmacies performing prospective DUR without computers are expected to...) A description of the steps taken by the State Agency to monitor compliance by pharmacies with the... entities such as the Medicaid Fraud Control Unit and State Board of Pharmacy. The annual report also must...

42 CFR 456.712 - Annual report.

Code of Federal Regulations, 2011 CFR

2011-10-01

... program. (2) A description of how pharmacies performing prospective DUR without computers are expected to...) A description of the steps taken by the State Agency to monitor compliance by pharmacies with the... entities such as the Medicaid Fraud Control Unit and State Board of Pharmacy. The annual report also must...

42 CFR 456.712 - Annual report.

Code of Federal Regulations, 2012 CFR

2012-10-01

... program. (2) A description of how pharmacies performing prospective DUR without computers are expected to...) A description of the steps taken by the State Agency to monitor compliance by pharmacies with the... entities such as the Medicaid Fraud Control Unit and State Board of Pharmacy. The annual report also must...

76 FR 3622 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-20

...: ER10-149-005, ER05-487-010, ER09-832-013. Applicants: Elk City Wind, LLC, FPL Energy Cowboy Wind, LLC, NexEra Energy Power Marketing, LLC. Description: NextEra Energy Entities Notification of Non-Material... Power Corporation. Description: Triennial Market Power Analysis of Vermont Yankee Nuclear Power...

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats

PubMed Central

Ison, Jon; Kalaš, Matúš; Jonassen, Inge; Bolser, Dan; Uludag, Mahmut; McWilliam, Hamish; Malone, James; Lopez, Rodrigo; Pettifer, Steve; Rice, Peter

2013-01-01

Motivation: Advancing the search, publication and integration of bioinformatics tools and resources demands consistent machine-understandable descriptions. A comprehensive ontology allowing such descriptions is therefore required. Results: EDAM is an ontology of bioinformatics operations (tool or workflow functions), types of data and identifiers, application domains and data formats. EDAM supports semantic annotation of diverse entities such as Web services, databases, programmatic libraries, standalone tools, interactive applications, data schemas, datasets and publications within bioinformatics. EDAM applies to organizing and finding suitable tools and data and to automating their integration into complex applications or workflows. It includes over 2200 defined concepts and has successfully been used for annotations and implementations. Availability: The latest stable version of EDAM is available in OWL format from http://edamontology.org/EDAM.owl and in OBO format from http://edamontology.org/EDAM.obo. It can be viewed online at the NCBO BioPortal and the EBI Ontology Lookup Service. For documentation and license please refer to http://edamontology.org. This article describes version 1.2 available at http://edamontology.org/EDAM_1.2.owl. Contact: jison@ebi.ac.uk PMID:23479348

LispSEI: The Programmer’s Manual

DTIC Science & Technology

1988-01-01

defun print-entities ( str entities etype) (format t str ) (dolist (entity entities) (format t " -A" (entity-name entity *type)))) (detun entity-name...fields are munged only after the filters are executed. This makes things much easier. ;:Algorithm: (1) get initial list. (2) take out those entitles which...don’t meet all the constraints. 1, 3) pass the entities list through all the filters.(4) munge the appropriate fields (5)u return the result. (defn s

Individuation of objects and events: a developmental study.

PubMed

Wagner, Laura; Carey, Susan

2003-12-01

This study investigates children's ability to use language to guide their choice of individuation criterion in the domains of objects and events. Previous work (Shipley, E. F., & Shepperson, B. (1990). Countable entities: developmental changes. Cognition, 34, 109-136.) has shown that children have a strong bias to use a spatio-temporal individuation strategy when counting objects and that children will ignore a conflicting linguistic description in favor of this spatio-temporal bias. Experiment 1 asked children (3-, 4-, and 5-year-olds) and adults to count objects and events under different linguistic descriptions. In the object task, subjects counted pictures of familiar objects split into multiple pieces (as in Shipley, E. F., & Shepperson, B. (1990). Countable entities: developmental changes. Cognition, 34, 109-136.) and described either using an appropriate kind label (e.g. "car") or the general term "thing". In the event task, subjects watched short animated movies consisting of a goal-oriented event achieved via multiple, temporally separated steps. The events were described either with an appropriate telic predicate targeting the goal (e.g. "paint a flower") or with an atelic predicate targeting the steps in the process (e.g. "paint") and the subjects' task was to count the events. Relative to adults, children preferred a spatio-temporal counting strategy in both tasks; there was no difference among the three groups of children. However, children were able to significantly change their counting strategy to follow the linguistic description in the event but not the object task. Experiment 2 extended the object task to include counting of other types of non-spatio-temporal units such as sub-parts of objects and collections. Results showed that children could use the linguistic descriptions to guide their counting strategy for these new items, though they continued to show a bias for a spatio-temporal individuation strategy with the collections. We suggest potential cognitive origins for the spatio-temporal individuation bias and how it interacts with children's developing linguistic knowledge.

77 FR 20296 - Significant New Use Rules on Certain Chemical Substances

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-04

.... Potentially affected entities may include, but are not limited to: Manufacturers, importers, or processors of... regarding entities likely to be affected by this action. Other types of entities not listed in this unit... of manufacturing and processing of a chemical substance. The extent to which a use changes the type...

Tumoral, quasitumoral and pseudotumoral lesions of the superficial and somatic soft tissue: new entities and new variants of old entities recorded during the last 25 years. Part XII: appendix.

PubMed

Bisceglia, M; Spagnolo, D; Galliani, C; Fisher, C; Suster, S; Kazakov, D V; Cooper, K; Michal, M

2006-08-01

In an eleven part series published in Pathologica, we have presented various tumoral, quasitumoral and pseudotumoral lesions of the superficial and somatic soft tissue (ST), which emerged as new entities or as variants of established entities during the last quarter of a century. Detailed clinicomorphological and differential diagnostic features of approximately sixty entities were chosen on the basis of their clinical significance and morphologic distinctiveness. The series included fibrous and myofibroblastic tumors (e.g. solitary fibrous tumor, high grade classic and pigmented dermatofibrosarcoma protuberans, inflammatory myofibroblastic tumor and myofibrosarcomas), fibromyxoid and fibrohistiocytic neoplasms (e.g., Evans' tumor, phosphaturic mesenchymal tumor, inflammatory myxohyaline tumor), special adipocytic/vascular/and smooth muscle lesions (e.g., chondroid lipoma, Dabska's tumor, ST hemangioblastoma, lipoleiomyosarcoma), epithelioid mesenchymal malignancies of diverse lineages (e.g., epithelioid liposarcoma, proximal-type epithelioid sarcoma, neuroendocrine extraskeletal chondromyxoid sarcoma), ST Ewing's tumor and peripheral nerve sheath tumors (perineuriomas and pigmented and rosetting tumors of the schwannoma/neurofibroma group), extranodal dendritic or histiocytic proliferative processes (follicular dendritic cell sarcoma, Rosai-Dorfman disease, Castleman's disease, and plexiform xanthomatous tumor), and tumors with myoepithelial differentiation. The section devoted to selected pseudotumoral entities considered representatives of the hamartoma group (neural fibrolipomatous hamartoma, ectopic hamartomatous thymoma, rudimentary meningocele), metabolic diseases (amyloid tumor, nephrogenic fibrosing dermopathy, tophaceous pseudogout, pseudoinfiltrative parathyromatosis), stromal tissue reactions to trauma (fibroosseous pseudotumors of digits) and infections (bacillary angiomatosis), and normal organs (glomus coccygeum). To conclude the descriptive phase, supplementary material has now been collected and appended in an attempt to provide a quick digest of essential knowledge both for comparison and differential diagnosis. The data have been tailored to synthesize diverse sources, integrating clinical elements and references to articles that previously appeared in Part I ("Introduction"), Part II ("The List and Review of New Entities") and Parts III to XI ("Excerpta"). At the very least we hope this final part ("Appendix") will provide the reader with a useful tabular organization of ST lesions and a reference resource.

40 CFR 80.270 - Can a refiner seek temporary relief from the requirements of this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... following information: (i) Detailed description of efforts to obtain capital for refinery investments; (ii) Bond rating of entity that owns the refinery; and (iii) Estimated capital investment needed to comply... necessary for construction, a description of plans to obtain necessary capital, and a detailed estimate of...

75 FR 26193 - Notice of Funds Availability: Inviting Applications for the Technical Assistance for Specialty...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-11

.... The intended effect of this notice is to solicit applications from the private sector and from... description of relevant dates. FOR FURTHER INFORMATION CONTACT: Entities wishing to apply for funding.... Funding Opportunity Description Authority: The TASC program is authorized by section 3205 of Public Law...

76 FR 2268 - Viruses, Serums, Toxins, and Analogous Products; Packaging and Labeling

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-13

.... Effects on Small Entities The RFA requires agencies to evaluate the potential effects of their proposed... and placed giving equal emphasis to each word composing it. Descriptive terms used in the true name on the product license or permit shall also appear. Abbreviations of the descriptive terms may be used on...

A Statistical Model for Multilingual Entity Detection and Tracking

DTIC Science & Technology

2004-01-01

tomatic Content Extraction ( ACE ) evaluation achieved top-tier results in all three evaluation languages. 1 Introduction Detecting entities, whether named...of com- bining the detected mentions into groups of references to the same object. The work presented here is motivated by the ACE eval- uation...Entropy (MaxEnt henceforth) (Berger et al., 1996) and Robust Risk Minimization (RRM henceforth) 1For a description of the ACE program see http

Digital geologic map database of the Nevada Test Site area, Nevada

USGS Publications Warehouse

Wahl, R.R.; Sawyer, D.A.; Minor, S.A.; Carr, M.D.; Cole, J.C.; Swadley, W.C.; Laczniak, R.J.; Warren, R.G.; Green, K.S.; Engle, C.M.

1997-01-01

Forty years of geologic investigations at the Nevada Test Site (NTS) have been digitized. These data include all geologic information that: (1) has been collected, and (2) can be represented on a map within the map borders at the map scale is included in the map digital coverages. The following coverages are included with this dataset: Coverage Type Description geolpoly Polygon Geologic outcrops geolflts line Fault traces geolatts Point Bedding attitudes, etc. geolcald line Caldera boundaries geollins line Interpreted lineaments geolmeta line Metamorphic gradients The above coverages are attributed with numeric values and interpreted information. The entity files documented below show the data associated with each coverage.

Malignant changes developing from odontogenic cysts: A systematic review.

PubMed

Borrás-Ferreres, Jordi; Sánchez-Torres, Alba; Gay-Escoda, Cosme

2016-12-01

The aim of this study was to systematically review scientific literature in orderto describe the characteristics and prognosis of malignant entities developing from odontogenic cysts. A search in Pubmed (MEDLINE) and Cochrane databases was conducted. The inclusion criteria were articles published in English related to the malignisation of odontogenic cysts in humans. The exclusion criteria were articles that do not specify the type of odontogenic cyst, malignisation of parakeratinised keratocysts, the presence of an ameloblastic carcinoma and metastasis from distant primary tumours. The selected articles were classified according to Strength of Recommendation Taxonomy criteria. Statistical analysis of the data was carried out using statistical package software SPSS version 22.0. From the 1,237 articles initially obtained, the authors included 3 case series and 45 case reports in the end. Descriptive analysis showed that men have a disposition for malignisation from odontogenic cysts and they frequently appear at the posterior mandible, with pain and swelling being the most frequent signs and symptoms. Follicular cysts were the entities that underwent the most malignant changes with well differentiated squamous cell carcinomas being the most prevalent type of malignancy. The real prognosis of this malignancy is not known because of the heterogeneity of available studies. Key words: Odontogenic cysts, squamous cell carcinoma, neoplastic cell transformation, oral cancer.

Karl Jaspers on the disease entity: Kantian ideas and Weberian ideal types.

PubMed

Walker, Chris

2014-09-01

Jaspers' nosology is indebted to Immanuel Kant's theory of knowledge. He drew the distinction of form and content from the Transcendental Analytic of Kant's Critique of Pure Reason. The distinction is universal to all knowledge, including psychopathology. Individual experience is constituted by a form or category of the Understanding to give a determinate or knowable object classified into the generic type of a real disease entity. The application of form and content is limited by the boundaries of experience. Beyond this boundary are wholes whose conception requires Ideas of reason drawn from the Transcendental Dialectic. Wholes are regulated by Ideas of reason to give an object or schema of the Idea collected into ideal types of an ideal typical disease entity. Jaspers drew ideal types from Max Weber's social theory. He anticipated that, as knowledge advanced, ideal typical disease entities would become real disease entities. By 1920, this had been the destiny of general paralysis as knowledge of its neuropathology, serology and microbiology emerged. As he presented the final edition of General Psychopathology in 1946, Jaspers was anticipating the transition of schizophrenia from ideal typical to real disease entity. Almost 70 years later, with knowledge of its aetiology still unclear, schizophrenia remains marooned as an ideal typical disease entity - still awaiting that crucial advance! © The Author(s) 2014.

2 CFR 25.110 - Types of recipient and subrecipient entities to which this part applies.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 2 Grants and Agreements 1 2012-01-01 2012-01-01 false Types of recipient and subrecipient entities... agency awards; or (2) Receive subawards directly from recipients of those agency awards. (b) Exemptions... identified in paragraph (d)(2) of this section, an agency may exempt an entity from an applicable requirement...

2 CFR 25.110 - Types of recipient and subrecipient entities to which this part applies.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 2 Grants and Agreements 1 2014-01-01 2014-01-01 false Types of recipient and subrecipient entities... (2) Receive subawards directly from recipients of those agency awards. (b) Exemptions for individuals... in paragraph (d)(2) of this section, an agency may exempt an entity from an applicable requirement to...

2 CFR 170.110 - Types of entities to which this part applies.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 2 Grants and Agreements 1 2014-01-01 2014-01-01 false Types of entities to which this part applies... or receive agency awards; or (2) Receive subawards under those awards. (b) Exceptions. (1) None of... her name). (2) None of the requirements regarding reporting names and total compensation of an entity...

2 CFR 25.110 - Types of recipient and subrecipient entities to which this part applies.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 2 Grants and Agreements 1 2013-01-01 2013-01-01 false Types of recipient and subrecipient entities... agency awards; or (2) Receive subawards directly from recipients of those agency awards. (b) Exemptions... identified in paragraph (d)(2) of this section, an agency may exempt an entity from an applicable requirement...

2 CFR 25.110 - Types of recipient and subrecipient entities to which this part applies.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 2 Grants and Agreements 1 2011-01-01 2011-01-01 false Types of recipient and subrecipient entities... agency awards; or (2) Receive subawards directly from recipients of those agency awards. (b) Exemptions... identified in paragraph (d)(2) of this section, an agency may exempt an entity from an applicable requirement...

2 CFR 170.110 - Types of entities to which this part applies.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 2 Grants and Agreements 1 2011-01-01 2011-01-01 false Types of entities to which this part applies... or receive agency awards; or (2) Receive subawards under those awards. (b) Exceptions. (1) None of... her name). (2) None of the requirements regarding reporting names and total compensation of an entity...

Category mistakes: A barrier to effective environmental management.

PubMed

Wallace, Ken J; Jago, Mark

2017-09-01

How entities, the things that exist, are defined and categorised affects all aspects of environmental management including technical descriptions, quantitative analyses, participatory processes, planning, and decisions. Consequently, ambiguous definitions and wrongly assigning entities to categories, referred to as category mistakes, are barriers to effective management. Confusion caused by treating the term 'biodiversity' variously as the property of an area, the biota of an area, and a preferred end state (a value) - quite different categories of entities - is one example. To overcome such difficulties, we develop and define four entity categories - elements, processes, properties, and values - and two derived categories - states and systems. We argue that adoption of these categories and definitions will significantly improve environmental communication and analysis, and thus strengthen planning and decision-making. Copyright © 2017 Elsevier Ltd. All rights reserved.

Community Digital Library Requirements for the Southern California Earthquake Center Community Modeling Environment (SCEC/CME)

NASA Astrophysics Data System (ADS)

Moore, R.; Faerman, M.; Minster, J.; Day, S. M.; Ely, G.

2003-12-01

A community digital library provides support for ingestion, organization, description, preservation, and access of digital entities. The technologies that traditionally provide these capabilities are digital libraries (ingestion, organization, description), persistent archives (preservation) and data grids (access). We present a design for the SCEC community digital library that incorporates aspects of all three systems. Multiple groups have created integrated environments that sustain large-scale scientific data collections. By examining these projects, the following stages of implementation can be identified: \\begin{itemize} Definition of semantic terms to associate with relevant information. This includes definition of uniform content descriptors to describe physical quantities relevant to the scientific discipline, and creation of concept spaces to define how the uniform content descriptors are logically related. Organization of digital entities into logical collections that make it simple to browse and manage related material. Definition of services that are used to access and manipulate material in the collection. Creation of a preservation environment for the long-term management of the collection. Each community is faced with heterogeneity that is introduced when data is distributed across multiple sites, or when multiple sets of collection semantics are used, and or when multiple scientific sub-disciplines are federated. We will present the relevant standards that simplify the implementation of the SCEC community library, the resource requirements for different types of data sets that drive the implementation, and the digital library processes that the SCEC community library will support. The SCEC community library can be viewed as the set of processing steps that are required to build the appropriate SCEC reference data sets (SCEC approved encoding format, SCEC approved descriptive metadata, SCEC approved collection organization, and SCEC managed storage location). Each digital entity that is ingested into the SCEC community library is processed and validated for conformance to SCEC standards. These steps generate provenance, descriptive, administrative, structural, and behavioral metadata. Using data grid technology, the descriptive metadata can be registered onto a logical name space that is controlled and managed by the SCEC digital library. A version of the SCEC community digital library is being implemented in the Storage Resource Broker. The SRB system provides almost all the features enumerated above. The peer-to-peer federation of metadata catalogs is planned for release in September, 2003. The SRB system is in production use in multiple projects, from high-energy physics, to astronomy, to earth systems science, to bio-informatics. The SCEC community library will be based on the definition of standard metadata attributes, the creation of logical collections within the SRB, the creation of access services, and the demonstration of a preservation environment. The use of the SRB for the SCEC digital library will sustain the expected collection size and collection capabilities.

In-toeing in children with type I osteogenesis imperfecta: an observational descriptive study.

PubMed

Losa Iglesias, Marta Elena; Becerro de Bengoa Vallejo, Ricardo; Salvadores Fuentes, Paloma

2009-01-01

Osteogenesis imperfecta is an autosomal-dominant disorder of the connective tissue. Also known as brittle bone disease, it renders those affected susceptible to fractures after minimal trauma. Therefore, it is important to minimize the risk of falls and subsequent fractures in patients with this disease. In-toeing is a common condition in children that can result from various pathologic entities, including anteversion, internal tibial torsion, and metatarsus adductus. These conditions can result in frequent tripping and other functional problems. A descriptive study was undertaken to determine the prevalence of in-toeing gait attributable to tibial or femoral torsion or metatarsus adductus in children with type I osteogenesis imperfecta. The study involved orthopedic and biomechanical examination of 15 children (9 girls and 6 boys) aged 4 to 9 years with confirmed type I osteogenesis imperfecta. Patients who used assistive ambulatory devices, such as canes, crutches, and wheelchairs, were excluded from the study. Of the 15 children studied, 12 (80%) demonstrated previously undiagnosed in-toeing gait attributable to torsional deformity or metatarsus adductus in all but one child. Many children with confirmed type I osteogenesis imperfecta have in-toeing gait caused by torsional deformity or metatarsus adductus. Detection and control of in-toeing gait in children with osteogenesis imperfecta is important to prevent fractures resulting from trauma directly related to these conditions.

19 CFR 123.71 - Description of program.

Code of Federal Regulations, 2010 CFR

2010-04-01

... voluntary cooperation of commercial conveyance entities in Customs effort to prevent the smuggling of... closely with Customs in identifying and reporting suspected smuggling attempts. In exchange for this...

Integrating Language and Vision to Generate Natural Language Descriptions of Videos in the Wild

DTIC Science & Technology

2014-08-23

the videos and produce probabilistic detections of grammatical subjects, verbs, and objects. In our data-set there are 45 candidate entities for the... grammatical subject (such as animal, baby, cat, chef, and person) and 241 for the grammatical object (such as flute, motorbike, shrimp, person, and tv...There are 218 candidate activities for the grammatical verb, including climb, cut, play, ride, and walk. Entity Related Features From each video two

47 CFR 101.1440 - MVDDS protection of DBS.

Code of Federal Regulations, 2010 CFR

2010-10-01

... along with main beam azimuth and altitude orientation information, and description of the antenna... responsible for providing information they deem necessary for those entities who install all future DBS...

Supervised segmentation of phenotype descriptions for the human skeletal phenome using hybrid methods.

PubMed

Groza, Tudor; Hunter, Jane; Zankl, Andreas

2012-10-15

Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. In order to fully capture the intrinsic value and knowledge expressed within them, we need to take advantage of their inner structure, which implicitly combines qualities and anatomical entities. The first step in this process is the segmentation of the phenotype descriptions into their atomic elements. We present a two-phase hybrid segmentation method that combines a series individual classifiers using different aggregation schemes (set operations and simple majority voting). The approach is tested on a corpus comprised of skeletal phenotype descriptions emerged from the Human Phenotype Ontology. Experimental results show that the best hybrid method achieves an F-Score of 97.05% in the first phase and F-Scores of 97.16% / 94.50% in the second phase. The performance of the initial segmentation of anatomical entities and qualities (phase I) is not affected by the presence / absence of external resources, such as domain dictionaries. From a generic perspective, hybrid methods may not always improve the segmentation accuracy as they are heavily dependent on the goal and data characteristics.

My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development.

PubMed

Rabattu, Pierre-Yves; Massé, Benoit; Ulliana, Federico; Rousset, Marie-Christine; Rohmer, Damien; Léon, Jean-Claude; Palombi, Olivier

2015-01-01

Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos. Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human developmental anatomy. Visualizing embryos with 3D geometric models and their animated deformations perhaps paves the way towards some kind of hypothesis-driven application. These can also be used to assist the learning process of this complex knowledge. http://www.mycorporisfabrica.org/.

Unsupervised Biomedical Named Entity Recognition: Experiments with Clinical and Biological Texts

PubMed Central

Zhang, Shaodian; Elhadad, Nóemie

2013-01-01

Named entity recognition is a crucial component of biomedical natural language processing, enabling information extraction and ultimately reasoning over and knowledge discovery from text. Much progress has been made in the design of rule-based and supervised tools, but they are often genre and task dependent. As such, adapting them to different genres of text or identifying new types of entities requires major effort in re-annotation or rule development. In this paper, we propose an unsupervised approach to extracting named entities from biomedical text. We describe a stepwise solution to tackle the challenges of entity boundary detection and entity type classification without relying on any handcrafted rules, heuristics, or annotated data. A noun phrase chunker followed by a filter based on inverse document frequency extracts candidate entities from free text. Classification of candidate entities into categories of interest is carried out by leveraging principles from distributional semantics. Experiments show that our system, especially the entity classification step, yields competitive results on two popular biomedical datasets of clinical notes and biological literature, and outperforms a baseline dictionary match approach. Detailed error analysis provides a road map for future work. PMID:23954592

Dynamic Data Management Based on Archival Process Integration at the Centre for Environmental Data Archival

NASA Astrophysics Data System (ADS)

Conway, Esther; Waterfall, Alison; Pepler, Sam; Newey, Charles

2015-04-01

In this paper we decribe a business process modelling approach to the integration of exisiting archival activities. We provide a high level overview of existing practice and discuss how procedures can be extended and supported through the description of preservation state. The aim of which is to faciliate the dynamic controlled management of scientific data through its lifecycle. The main types of archival processes considered are: • Management processes that govern the operation of an archive. These management processes include archival governance (preservation state management, selection of archival candidates and strategic management) . • Operational processes that constitute the core activities of the archive which maintain the value of research assets. These operational processes are the acquisition, ingestion, deletion, generation of metadata and preservation actvities, • Supporting processes, which include planning, risk analysis and monitoring of the community/preservation environment. We then proceed by describing the feasability testing of extended risk management and planning procedures which integrate current practices. This was done through the CEDA Archival Format Audit which inspected British Atmospherics Data Centre and National Earth Observation Data Centre Archival holdings. These holdings are extensive, comprising of around 2PB of data and 137 million individual files which were analysed and characterised in terms of format based risk. We are then able to present an overview of the risk burden faced by a large scale archive attempting to maintain the usability of heterogeneous environmental data sets. We conclude by presenting a dynamic data management information model that is capable of describing the preservation state of archival holdings throughout the data lifecycle. We provide discussion of the following core model entities and their relationships: • Aspirational entities, which include Data Entity definitions and their associated Preservation Objectives. • Risk entities, which act as drivers for change within the data lifecycle. These include Acquisitional Risks, Technical Risks, Strategic Risks and External Risks • Plan entities, which detail the actions to bring about change within an archive. These include Acquisition Plans, Preservation Plans and Monitoring plans • The Result entities describe the successful outcomes of the executed plans. These include Acquisitions, Mitigations and Accepted Risks.

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation.

PubMed

Malone, James; Brown, Andy; Lister, Allyson L; Ison, Jon; Hull, Duncan; Parkinson, Helen; Stevens, Robert

2014-01-01

Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility. The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications. The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user's needs. The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com.

The Software Ontology (SWO): a resource for reproducibility in biomedical data analysis, curation and digital preservation

PubMed Central

2014-01-01

Motivation Biomedical ontologists to date have concentrated on ontological descriptions of biomedical entities such as gene products and their attributes, phenotypes and so on. Recently, effort has diversified to descriptions of the laboratory investigations by which these entities were produced. However, much biological insight is gained from the analysis of the data produced from these investigations, and there is a lack of adequate descriptions of the wide range of software that are central to bioinformatics. We need to describe how data are analyzed for discovery, audit trails, provenance and reproducibility. Results The Software Ontology (SWO) is a description of software used to store, manage and analyze data. Input to the SWO has come from beyond the life sciences, but its main focus is the life sciences. We used agile techniques to gather input for the SWO and keep engagement with our users. The result is an ontology that meets the needs of a broad range of users by describing software, its information processing tasks, data inputs and outputs, data formats versions and so on. Recently, the SWO has incorporated EDAM, a vocabulary for describing data and related concepts in bioinformatics. The SWO is currently being used to describe software used in multiple biomedical applications. Conclusion The SWO is another element of the biomedical ontology landscape that is necessary for the description of biomedical entities and how they were discovered. An ontology of software used to analyze data produced by investigations in the life sciences can be made in such a way that it covers the important features requested and prioritized by its users. The SWO thus fits into the landscape of biomedical ontologies and is produced using techniques designed to keep it in line with user’s needs. Availability The Software Ontology is available under an Apache 2.0 license at http://theswo.sourceforge.net/; the Software Ontology blog can be read at http://softwareontology.wordpress.com. PMID:25068035

10 CFR 300.8 - Calculating emission reductions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... household operation; and (4) A description of the emission sources or sinks covered, such as fossil fuel... the specific form of benefit or relief provided. (k) Determining the entity responsible for emission...

10 CFR 300.8 - Calculating emission reductions.

Code of Federal Regulations, 2014 CFR

2014-01-01

... household operation; and (4) A description of the emission sources or sinks covered, such as fossil fuel... the specific form of benefit or relief provided. (k) Determining the entity responsible for emission...

10 CFR 300.8 - Calculating emission reductions.

Code of Federal Regulations, 2012 CFR

2012-01-01

... household operation; and (4) A description of the emission sources or sinks covered, such as fossil fuel... the specific form of benefit or relief provided. (k) Determining the entity responsible for emission...

10 CFR 300.8 - Calculating emission reductions.

Code of Federal Regulations, 2011 CFR

2011-01-01

... household operation; and (4) A description of the emission sources or sinks covered, such as fossil fuel... the specific form of benefit or relief provided. (k) Determining the entity responsible for emission...

10 CFR 300.8 - Calculating emission reductions.

Code of Federal Regulations, 2013 CFR

2013-01-01

... household operation; and (4) A description of the emission sources or sinks covered, such as fossil fuel... the specific form of benefit or relief provided. (k) Determining the entity responsible for emission...

Structure Discovery in Large Semantic Graphs Using Extant Ontological Scaling and Descriptive Statistics

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

al-Saffar, Sinan; Joslyn, Cliff A.; Chappell, Alan R.

As semantic datasets grow to be very large and divergent, there is a need to identify and exploit their inherent semantic structure for discovery and optimization. Towards that end, we present here a novel methodology to identify the semantic structures inherent in an arbitrary semantic graph dataset. We first present the concept of an extant ontology as a statistical description of the semantic relations present amongst the typed entities modeled in the graph. This serves as a model of the underlying semantic structure to aid in discovery and visualization. We then describe a method of ontological scaling in which themore » ontology is employed as a hierarchical scaling filter to infer different resolution levels at which the graph structures are to be viewed or analyzed. We illustrate these methods on three large and publicly available semantic datasets containing more than one billion edges each. Keywords-Semantic Web; Visualization; Ontology; Multi-resolution Data Mining;« less

A data model for environmental scientists

NASA Astrophysics Data System (ADS)

Kapeljushnik, O.; Beran, B.; Valentine, D.; van Ingen, C.; Zaslavsky, I.; Whitenack, T.

2008-12-01

Environmental science encompasses a wide range of disciplines from water chemistry to microbiology, ecology and atmospheric sciences. Studies often require working across disciplines which differ in their ways of describing and storing data such that it is not possible to devise a monolithic one-size-fits-all data solution. Based on our experiences with Consortium of the Universities for the Advancement of Hydrologic Science Inc. (CUAHSI) Observations Data Model, Berkeley Water Center FLUXNET carbon-climate work and by examining standards like EPA's Water Quality Exchange (WQX), we have developed a flexible data model that allows extensions without need to altering the schema such that scientists can define custom metadata elements to describe their data including observations, analysis methods as well as sensors and geographical features. The data model supports various types of observations including fixed point and moving sensors, bottled samples, rasters from remote sensors and models, and categorical descriptions (e.g. taxonomy) by employing user-defined-types when necessary. It leverages ADO .NET Entity Framework to provide the semantic data models for differing disciplines, while maintaining a common schema below the entity layer. This abstraction layer simplifies data retrieval and manipulation by hiding the logic and complexity of the relational schema from users thus allows programmers and scientists to deal directly with objects such as observations, sensors, watersheds, river reaches, channel cross-sections, laboratory analysis methods and samples as opposed to table joins, columns and rows.

Rosette-forming glioneuronal tumor of the fourth ventricle.

PubMed

Preusser, Matthias; Dietrich, Wolfgang; Czech, Thomas; Prayer, Daniela; Budka, Herbert; Hainfellner, Johannes A

2003-11-01

Rosette-forming glioneuronal tumor (RGNT) of the fourth ventricle has been reported recently as a novel type of primary CNS neoplasm. We present the case of a 35-year-old male patient with RGNT of the fourth ventricle. The tumor was found incidentally; the patient did not suffer from any neurological symptoms. The tumor mass involved the caudal cerebellar vermis, filled the fourth ventricle and protruded into the caudal part of the mesencephalic aquaeduct. Smaller tumor nodules were visible in the adjacent right cerebellar hemisphere. Histologically, prominent neurocytic rosettes with synaptophysin expression were embedded in a glial tumor component resembling pilocytic astrocytoma. Clinicopathological features of our case closely resemble those reported in the original description. Thus, our case confirms RGNT as a new distinct type of primary CNS neoplasm. Due to its distinct features, adoption of RGNT as a new entity into the WHO classification of tumors should be considered.

Discovery of Predicate-Oriented Relations among Named Entities Extracted from Thai Texts

NASA Astrophysics Data System (ADS)

Tongtep, Nattapong; Theeramunkong, Thanaruk

Extracting named entities (NEs) and their relations is more difficult in Thai than in other languages due to several Thai specific characteristics, including no explicit boundaries for words, phrases and sentences; few case markers and modifier clues; high ambiguity in compound words and serial verbs; and flexible word orders. Unlike most previous works which focused on NE relations of specific actions, such as work_for, live_in, located_in, and kill, this paper proposes more general types of NE relations, called predicate-oriented relation (PoR), where an extracted action part (verb) is used as a core component to associate related named entities extracted from Thai Texts. Lacking a practical parser for the Thai language, we present three types of surface features, i.e. punctuation marks (such as token spaces), entity types and the number of entities and then apply five alternative commonly used learning schemes to investigate their performance on predicate-oriented relation extraction. The experimental results show that our approach achieves the F-measure of 97.76%, 99.19%, 95.00% and 93.50% on four different types of predicate-oriented relation (action-location, location-action, action-person and person-action) in crime-related news documents using a data set of 1,736 entity pairs. The effects of NE extraction techniques, feature sets and class unbalance on the performance of relation extraction are explored.

Anatomical Entity Recognition with a Hierarchical Framework Augmented by External Resources

PubMed Central

Xu, Yan; Hua, Ji; Ni, Zhaoheng; Chen, Qinlang; Fan, Yubo; Ananiadou, Sophia; Chang, Eric I-Chao; Tsujii, Junichi

2014-01-01

References to anatomical entities in medical records consist not only of explicit references to anatomical locations, but also other diverse types of expressions, such as specific diseases, clinical tests, clinical treatments, which constitute implicit references to anatomical entities. In order to identify these implicit anatomical entities, we propose a hierarchical framework, in which two layers of named entity recognizers (NERs) work in a cooperative manner. Each of the NERs is implemented using the Conditional Random Fields (CRF) model, which use a range of external resources to generate features. We constructed a dictionary of anatomical entity expressions by exploiting four existing resources, i.e., UMLS, MeSH, RadLex and BodyPart3D, and supplemented information from two external knowledge bases, i.e., Wikipedia and WordNet, to improve inference of anatomical entities from implicit expressions. Experiments conducted on 300 discharge summaries showed a micro-averaged performance of 0.8509 Precision, 0.7796 Recall and 0.8137 F1 for explicit anatomical entity recognition, and 0.8695 Precision, 0.6893 Recall and 0.7690 F1 for implicit anatomical entity recognition. The use of the hierarchical framework, which combines the recognition of named entities of various types (diseases, clinical tests, treatments) with information embedded in external knowledge bases, resulted in a 5.08% increment in F1. The resources constructed for this research will be made publicly available. PMID:25343498

Decomposing phenotype descriptions for the human skeletal phenome.

PubMed

Groza, Tudor; Hunter, Jane; Zankl, Andreas

2013-01-01

Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. The intrinsic value and knowledge captured within such descriptions can only be expressed by taking advantage of their inner structure that implicitly combines qualities and anatomical entities. We present a meta-model (the Phenotype Fragment Ontology) and a processing pipeline that enable together the automatic decomposition and conceptualization of phenotype descriptions for the human skeletal phenome. We use this approach to showcase the usefulness of the generic concept of phenotype decomposition by performing an experimental study on all skeletal phenotype concepts defined in the Human Phenotype Ontology.

Lichen planus hypertrophicus of the vulva - a rare entity.

PubMed

Job, Anupa Mary; Kaimal, Sowmya

2017-09-01

Vulvovaginal lichen planus is a type of chronic inflammatory dermatosis of the vulva, usually seen as a part of widespread lichen planus. The common clinical types of vulval lichen planus include papulosquamous, erosive and pigmented types. Hypertrophic lichen planus of the vulva is a rare entity. We report a case of hypertrophic lichen planus of the vulva which clinically simulated genital warts.

Vasculitis mimics.

PubMed

Molloy, Eamonn S; Langford, Carol A

2008-01-01

There are many disorders that may closely resemble the clinical, radiologic and/or pathologic features of the primary vasculitides. In this review, we focus on recently described and under-recognized syndromes that may mimic vasculitis. Hereditary causes of large-artery aneurysms such as Marfan's syndrome have long been recognized; recent years have seen a greater understanding of the genetics of Marfan's and other such disorders, including Loeys-Dietz syndrome and Ehler-Danlos syndrome type IV. Under-recognized mimics of medium-vessel vasculitis include segmental arterial mediolysis and Grange syndrome. A large number of entities can mimic small-vessel vasculitis. Recent descriptions of antibodies to human neutrophil elastase have provided insight into the occurrence of antineutrophil cytoplasmic antibodies in cocaine-induced midline destructive lesions. The differential diagnosis of cerebral vasculitis can be particularly difficult. Reversible cerebral vasoconstriction syndromes represent an important class of entities that can readily mimic cerebral vasculitis but have a very different management approach and outcome. The diagnosis of vasculitis requires careful assessment of all available clinical, laboratory, radiologic and pathologic information, and consideration of many competing differential diagnoses. Awareness of noninflammatory mimics of vasculitis is essential to avoid unnecessary and potentially harmful treatment with immunosuppressive agents.

Exploring Contextual Models in Chemical Patent Search

NASA Astrophysics Data System (ADS)

Urbain, Jay; Frieder, Ophir

We explore the development of probabilistic retrieval models for integrating term statistics with entity search using multiple levels of document context to improve the performance of chemical patent search. A distributed indexing model was developed to enable efficient named entity search and aggregation of term statistics at multiple levels of patent structure including individual words, sentences, claims, descriptions, abstracts, and titles. The system can be scaled to an arbitrary number of compute instances in a cloud computing environment to support concurrent indexing and query processing operations on large patent collections.

A study of machine-learning-based approaches to extract clinical entities and their assertions from discharge summaries.

PubMed

Jiang, Min; Chen, Yukun; Liu, Mei; Rosenbloom, S Trent; Mani, Subramani; Denny, Joshua C; Xu, Hua

2011-01-01

The authors' goal was to develop and evaluate machine-learning-based approaches to extracting clinical entities-including medical problems, tests, and treatments, as well as their asserted status-from hospital discharge summaries written using natural language. This project was part of the 2010 Center of Informatics for Integrating Biology and the Bedside/Veterans Affairs (VA) natural-language-processing challenge. The authors implemented a machine-learning-based named entity recognition system for clinical text and systematically evaluated the contributions of different types of features and ML algorithms, using a training corpus of 349 annotated notes. Based on the results from training data, the authors developed a novel hybrid clinical entity extraction system, which integrated heuristic rule-based modules with the ML-base named entity recognition module. The authors applied the hybrid system to the concept extraction and assertion classification tasks in the challenge and evaluated its performance using a test data set with 477 annotated notes. Standard measures including precision, recall, and F-measure were calculated using the evaluation script provided by the Center of Informatics for Integrating Biology and the Bedside/VA challenge organizers. The overall performance for all three types of clinical entities and all six types of assertions across 477 annotated notes were considered as the primary metric in the challenge. Systematic evaluation on the training set showed that Conditional Random Fields outperformed Support Vector Machines, and semantic information from existing natural-language-processing systems largely improved performance, although contributions from different types of features varied. The authors' hybrid entity extraction system achieved a maximum overall F-score of 0.8391 for concept extraction (ranked second) and 0.9313 for assertion classification (ranked fourth, but not statistically different than the first three systems) on the test data set in the challenge.

New daily persistent headache: a syndrome, not a discrete disorder.

PubMed

Goadsby, Peter J

2011-04-01

The term New Daily Persistent Headache (NDPH) has been used for nearly 25 years and yet the entity remains enigmatic. It can be argued the simplest, indeed most appropriate, approach is to use the term to mean simply what it says- i.e. as an umbrella description, rather like chronic daily headache. NDPH should be used as a diagnostic umbrella inviting better characterization, not be an achievement in itself. This would mean the term required no further elaboration- there would be no mimics- simply primary and secondary NDPH. A detailed examination of the literature reveals considerable heterogeneity in the phenotypic descriptions labelled as NDPH. The first effort in a patient with a NDPH presentation is to discern if secondary causes are present; some are obvious, such as subarachnoid bleeds and some can be more troublesome, such as syndromes of abnormal CSF pressure/volume, either high or low. A cohort of primary NDPH headaches can be seen in practice and in the literature and these should be sub-divided into a migrainous type, with appropriate phenotypic manifestations and a featureless type. Patients with any one of the NDPH presentations are best managed according to the more detailed pathophysiology-based diagnosis then lumped together into a single group, since a single disorder is unlikely to exist. © 2011 American Headache Society.

75 FR 5077 - Pesticide Product; Registration Application

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-01

... affected by this action if you are an agricultural producer, food manufacturer, or pesticide manufacturer. Potentially affected entities may include, but are not limited to: Crop production (NAICS code 111). Animal... entities likely to be affected by this action. Other types of entities not listed in this unit could also...

Of Substance: The Nature of Language Effects on Entity Construal

PubMed Central

Li, Peggy; Dunham, Yarrow; Carey, Susan

2009-01-01

Shown an entity (e.g., a plastic whisk) labeled by a novel noun in neutral syntax, speakers of Japanese, a classifier language, are more likely to assume the noun refers to the substance (plastic) than are speakers of English, a count/mass language, who are instead more likely to assume it refers to the object kind (whisk; Imai and Gentner, 1997). Five experiments replicated this language type effect on entity construal, extended it to quite different stimuli from those studied before, and extended it to a comparison between Mandarin-speakers and English-speakers. A sixth experiment, which did not involve interpreting the meaning of a noun or a pronoun that stands for a noun, failed to find any effect of language type on entity construal. Thus, the overall pattern of findings supports a non-Whorfian, language on language account, according to which sensitivity to lexical statistics in a count/mass language leads adults to assign a novel noun in neutral syntax the status of a count noun, influencing construal of ambiguous entities. The experiments also document and explore cross-linguistically universal factors that influence entity construal, and favor Prasada's (1999) hypothesis that features indicating non-accidentalness of an entity's form lead participants to a construal of object-kind rather than substance-kind. Finally, the experiments document the age at which the language type effect emerges in lexical projection. The details of the developmental pattern are consistent with the lexical statistics hypothesis, along with a universal increase in sensitivity to material kind. PMID:19230873

14 CFR 291.44 - BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity.

Code of Federal Regulations, 2011 CFR

2011-01-01

... TRANSPORTATION Reporting Rules § 291.44 BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity. (a) For the purposes of BTS schedule P-12(a), type of service shall be either scheduled service or... 14 Aeronautics and Space 4 2011-01-01 2011-01-01 false BTS Schedule P-12(a), Fuel Consumption by...

Pathologic and Radiologic Correlation of Adult Cystic Lung Disease: A Comprehensive Review

PubMed Central

Parimi, Vamsi; Taddonio, Michale; Kane, Joshua Robert; Yeldandi, Anjana

2017-01-01

The presence of pulmonary parenchymal cysts on computed tomography (CT) imaging presents a significant diagnostic challenge. The diverse range of possible etiologies can usually be differentiated based on the clinical setting and radiologic features. In fact, the advent of high-resolution CT has facilitated making a diagnosis solely on analysis of CT image patterns, thus averting the need for a biopsy. While it is possible to make a fairly specific diagnosis during early stages of disease evolution by its characteristic radiological presentation, distinct features may progress to temporally converge into relatively nonspecific radiologic presentations sometimes necessitating histological examination to make a diagnosis. The aim of this review study is to provide both the pathologist and the radiologist with an overview of the diseases most commonly associated with cystic lung lesions primarily in adults by illustration and description of pathologic and radiologic features of each entity. Brief descriptions and characteristic radiologic features of the various disease entities are included and illustrative examples are provided for the common majority of them. In this article, we also classify pulmonary cystic disease with an emphasis on the pathophysiology behind cyst formation in an attempt to elucidate the characteristics of similar cystic appearances seen in various disease entities. PMID:28270943

Crossmaps: Visualization of overlapping relationships in collections of journal papers

PubMed Central

Morris, Steven A.; Yen, Gary G.

2004-01-01

A crossmapping technique is introduced for visualizing multiple and overlapping relations among entity types in collections of journal articles. Groups of entities from two entity types are crossplotted to show correspondence of relations. For example, author collaboration groups are plotted on the x axis against groups of papers (research fronts) on the y axis. At the intersection of each pair of author group/research front pairs a circular symbol is plotted whose size is proportional to the number of times that authors in the group appear as authors in papers in the research front. Entity groups are found by agglomerative hierarchical clustering using conventional similarity measures. Crossmaps comprise a simple technique that is particularly suited to showing overlap in relations among entity groups. Particularly useful crossmaps are: research fronts against base reference clusters, research fronts against author collaboration groups, and research fronts against term co-occurrence clusters. When exploring the knowledge domain of a collection of journal papers, it is useful to have several crossmaps of different entity pairs, complemented by research front timelines and base reference cluster timelines. PMID:14762168

2 CFR 170.110 - Types of entities to which this part applies.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 2 Grants and Agreements 1 2013-01-01 2013-01-01 false Types of entities to which this part applies...) Apply for or receive agency awards; or (2) Receive subawards under those awards. (b) Exceptions. (1... his or her name). (2) None of the requirements regarding reporting names and total compensation of an...

2 CFR 170.110 - Types of entities to which this part applies.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 2 Grants and Agreements 1 2012-01-01 2012-01-01 false Types of entities to which this part applies...) Apply for or receive agency awards; or (2) Receive subawards under those awards. (b) Exceptions. (1... his or her name). (2) None of the requirements regarding reporting names and total compensation of an...

14 CFR 291.44 - BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., DEPARTMENT OF TRANSPORTATION (AVIATION PROCEEDINGS) ECONOMIC REGULATIONS CARGO OPERATIONS IN INTERSTATE AIR TRANSPORTATION Reporting Rules § 291.44 BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity. (a...) Each air carrier shall maintain records for each station showing the computation of fuel inventories...

Thoracoscopic treatment of congenital esophageal stenosis in combination with H-type tracheoesophageal fistula.

PubMed

van Poll, Daan; van der Zee, David C

2012-08-01

Congenital esophageal stenosis combined with H-type tracheoesophageal fistula is a rare clinical entity that is often not diagnosed until months or sometimes many years after birth. We present a case of a boy who presented both these entities and was treated by thoracoscopy. Copyright © 2012 Elsevier Inc. All rights reserved.

NELasso: Group-Sparse Modeling for Characterizing Relations Among Named Entities in News Articles.

PubMed

Tariq, Amara; Karim, Asim; Foroosh, Hassan

2017-10-01

Named entities such as people, locations, and organizations play a vital role in characterizing online content. They often reflect information of interest and are frequently used in search queries. Although named entities can be detected reliably from textual content, extracting relations among them is more challenging, yet useful in various applications (e.g., news recommending systems). In this paper, we present a novel model and system for learning semantic relations among named entities from collections of news articles. We model each named entity occurrence with sparse structured logistic regression, and consider the words (predictors) to be grouped based on background semantics. This sparse group LASSO approach forces the weights of word groups that do not influence the prediction towards zero. The resulting sparse structure is utilized for defining the type and strength of relations. Our unsupervised system yields a named entities' network where each relation is typed, quantified, and characterized in context. These relations are the key to understanding news material over time and customizing newsfeeds for readers. Extensive evaluation of our system on articles from TIME magazine and BBC News shows that the learned relations correlate with static semantic relatedness measures like WLM, and capture the evolving relationships among named entities over time.

Hashimoto thyroiditis: a century later.

PubMed

Ahmed, Rania; Al-Shaikh, Safa; Akhtar, Mohammed

2012-05-01

More than a century has passed since the first description of Hashimoto thyroiditis (HT) as a clinicopathologic entity. HT is an autoimmune disease in which a breakdown of immune tolerance is caused by interplay of a variety of immunologic, genetic, and environmental factors. Thyrocyte injury resulting from environmental factors results in expression of new or hidden epitopes that leads to proliferation of autoreactive T and B cells. Infiltration of thyroid by these cells results in HT. In addition to the usual type of HT, several variants such as the fibrous type and Riedal thyroiditis are also recognized. The most recently recognized variant is immunoglobulin G4(+) HT, which may occur as isolated thyroid limited disease or as part of a generalized Ig4-related sclerosing disease. The relationship between HT and Riedel thyroiditis remains unclear; however, recent evidence seems to suggest that it may also be part of the spectrum of Ig4-related sclerosing disease. HT is frequently associated with papillary thyroid carcinoma and may indeed be a risk factor for developing this type of cancer. The relationship between thyroid lymphoma and HT on the other hand appears well established.

Update from the 4th Edition of the World Health Organization Classification of Head and Neck Tumours: Tumors of the Salivary Gland.

PubMed

Seethala, Raja R; Stenman, Göran

2017-03-01

The salivary gland section in the 4th edition of the World Health Organization classification of head and neck tumors features the description and inclusion of several entities, the most significant of which is represented by (mammary analogue) secretory carcinoma. This entity was extracted mainly from acinic cell carcinoma based on recapitulation of breast secretory carcinoma and a shared ETV6-NTRK3 gene fusion. Also new is the subsection of "Other epithelial lesions," for which key entities include sclerosing polycystic adenosis and intercalated duct hyperplasia. Many entities have been compressed into their broader categories given clinical and morphologic similarities, or transitioned to a different grouping as was the case with low-grade cribriform cystadenocarcinoma reclassified as intraductal carcinoma (with the applied qualifier of low-grade). Specific grade has been removed from the names of the salivary gland entities such as polymorphous adenocarcinoma, providing pathologists flexibility in assigning grade and allowing for recognition of a broader spectrum within an entity. Cribriform adenocarcinoma of (minor) salivary gland origin continues to be divisive in terms of whether it should be recognized as a distinct category. This chapter also features new key concepts such as high-grade transformation. The new paradigm of translocations and gene fusions being common in salivary gland tumors is featured heavily in this chapter.

Immune Response to a Variable Pathogen: A Stochastic Model with Two Interlocked Darwinian Entities

PubMed Central

Kuhn, Christoph

2012-01-01

This paper presents the modeling of a host immune system, more precisely the immune effector cell and immune memory cell population, and its interaction with an invading pathogen population. It will tackle two issues of interest; on the one hand, in defining a stochastic model accounting for the inherent nature of organisms in population dynamics, namely multiplication with mutation and selection; on the other hand, in providing a description of pathogens that may vary their antigens through mutations during infection of the host. Unlike most of the literature, which models the dynamics with first-order differential equations, this paper proposes a Galton-Watson type branching process to describe stochastically by whole distributions the population dynamics of pathogens and immune cells. In the first model case, the pathogen of a given type is either eradicated or shows oscillatory chronic response. In the second model case, the pathogen shows variational behavior changing its antigen resulting in a prolonged immune reaction. PMID:23424603

Active Brownian Particles. From Individual to Collective Stochastic Dynamics

NASA Astrophysics Data System (ADS)

Romanczuk, P.; Bär, M.; Ebeling, W.; Lindner, B.; Schimansky-Geier, L.

2012-03-01

We review theoretical models of individual motility as well as collective dynamics and pattern formation of active particles. We focus on simple models of active dynamics with a particular emphasis on nonlinear and stochastic dynamics of such self-propelled entities in the framework of statistical mechanics. Examples of such active units in complex physico-chemical and biological systems are chemically powered nano-rods, localized patterns in reaction-diffusion system, motile cells or macroscopic animals. Based on the description of individual motion of point-like active particles by stochastic differential equations, we discuss different velocity-dependent friction functions, the impact of various types of fluctuations and calculate characteristic observables such as stationary velocity distributions or diffusion coefficients. Finally, we consider not only the free and confined individual active dynamics but also different types of interaction between active particles. The resulting collective dynamical behavior of large assemblies and aggregates of active units is discussed and an overview over some recent results on spatiotemporal pattern formation in such systems is given.

Immune response to a variable pathogen: a stochastic model with two interlocked Darwinian entities.

PubMed

Kuhn, Christoph

2012-01-01

This paper presents the modeling of a host immune system, more precisely the immune effector cell and immune memory cell population, and its interaction with an invading pathogen population. It will tackle two issues of interest; on the one hand, in defining a stochastic model accounting for the inherent nature of organisms in population dynamics, namely multiplication with mutation and selection; on the other hand, in providing a description of pathogens that may vary their antigens through mutations during infection of the host. Unlike most of the literature, which models the dynamics with first-order differential equations, this paper proposes a Galton-Watson type branching process to describe stochastically by whole distributions the population dynamics of pathogens and immune cells. In the first model case, the pathogen of a given type is either eradicated or shows oscillatory chronic response. In the second model case, the pathogen shows variational behavior changing its antigen resulting in a prolonged immune reaction.

Selected aspects of polycystic ovarian disease.

PubMed

Goldzieher, J W; Young, R L

1992-03-01

Although there is general agreement about the polycystic ovary as an anatomic entity, a classic description of an associated syndrome remains elusive. This lack of definition, however, has not impeded clinical investigation. This article focuses on the diagnosis, pathogenesis, hypotheses, and treatment of polycystic ovarian disease.

A SELECTIVE BIBLIOGRAPHY ON BRAIN-DAMAGED CHILDREN.

ERIC Educational Resources Information Center

Woods School for Exceptional Children, Langhorne, PA.

THIS SELECTIVE BIBLIOGRAPHY INCLUDES 317 ANNOTATED REFERENCES DEALING DIRECTLY WITH THE BEHAVIORAL CHARCTERISTICS OF CHILDREN WITH CEREBRAL DYSFUNCTION. REFERENCES HAVE APPEARED IN JOURNALS OR OTHER SOURCES AVAILABLE IN UNIVERSITY LIBRARIES. THE BIBLIOGRAPHY IS CLASSIFIED INTO SIX MAJOR DIVISIONS--(1) THE ENTITY AND ITS DESCRIPTION, (2) CLINICAL…

76 FR 72402 - Combined Notice of Filings #1

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-23

...-772-003. Applicants: ExxonMobil Baton Rouge Complex. Description: ExxonMobil Entities submits their... Bethlehem, LLC, Calpine Mid-Atlantic Generation, LLC, Calpine Mid Merit, LLC, Calpine New Jersey Generation... City Generation, L.P., Forward WindPower, LLC, Lookout WindPower, LLC, Midwest Generation, LLC...

Towards improving phenotype representation in OWL

PubMed Central

2012-01-01

Background Phenotype ontologies are used in species-specific databases for the annotation of mutagenesis experiments and to characterize human diseases. The Entity-Quality (EQ) formalism is a means to describe complex phenotypes based on one or more affected entities and a quality. EQ-based definitions have been developed for many phenotype ontologies, including the Human and Mammalian Phenotype ontologies. Methods We analyze formalizations of complex phenotype descriptions in the Web Ontology Language (OWL) that are based on the EQ model, identify several representational challenges and analyze potential solutions to address these challenges. Results In particular, we suggest a novel, role-based approach to represent relational qualities such as concentration of iron in spleen, discuss its ontological foundation in the General Formal Ontology (GFO) and evaluate its representation in OWL and the benefits it can bring to the representation of phenotype annotations. Conclusion Our analysis of OWL-based representations of phenotypes can contribute to improving consistency and expressiveness of formal phenotype descriptions. PMID:23046625

Did scarlet fever and rheumatic fever exist in Hippocrates' time?

PubMed

Quinn, R W

1991-01-01

Case histories recorded by Hippocrates around 400 B.C. describe the clinical manifestations of scarlet fever and rheumatic fever, although the entities are not identified by name. Although the descriptions are not as detailed or complete as they would be today, they strongly suggest the existence of scarlet fever and rheumatic fever at that time. Hippocrates' references to these illnesses were presumably the first to be documented and/or discovered, as a thorough search of the worldwide medical literature revealed no prior descriptions.

The Biological Big Bang model for the major transitions in evolution.

PubMed

Koonin, Eugene V

2007-08-20

Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal. I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB). A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis.

The Biological Big Bang model for the major transitions in evolution

PubMed Central

Koonin, Eugene V

2007-01-01

Background Major transitions in biological evolution show the same pattern of sudden emergence of diverse forms at a new level of complexity. The relationships between major groups within an emergent new class of biological entities are hard to decipher and do not seem to fit the tree pattern that, following Darwin's original proposal, remains the dominant description of biological evolution. The cases in point include the origin of complex RNA molecules and protein folds; major groups of viruses; archaea and bacteria, and the principal lineages within each of these prokaryotic domains; eukaryotic supergroups; and animal phyla. In each of these pivotal nexuses in life's history, the principal "types" seem to appear rapidly and fully equipped with the signature features of the respective new level of biological organization. No intermediate "grades" or intermediate forms between different types are detectable. Usually, this pattern is attributed to cladogenesis compressed in time, combined with the inevitable erosion of the phylogenetic signal. Hypothesis I propose that most or all major evolutionary transitions that show the "explosive" pattern of emergence of new types of biological entities correspond to a boundary between two qualitatively distinct evolutionary phases. The first, inflationary phase is characterized by extremely rapid evolution driven by various processes of genetic information exchange, such as horizontal gene transfer, recombination, fusion, fission, and spread of mobile elements. These processes give rise to a vast diversity of forms from which the main classes of entities at the new level of complexity emerge independently, through a sampling process. In the second phase, evolution dramatically slows down, the respective process of genetic information exchange tapers off, and multiple lineages of the new type of entities emerge, each of them evolving in a tree-like fashion from that point on. This biphasic model of evolution incorporates the previously developed concepts of the emergence of protein folds by recombination of small structural units and origin of viruses and cells from a pre-cellular compartmentalized pool of recombining genetic elements. The model is extended to encompass other major transitions. It is proposed that bacterial and archaeal phyla emerged independently from two distinct populations of primordial cells that, originally, possessed leaky membranes, which made the cells prone to rampant gene exchange; and that the eukaryotic supergroups emerged through distinct, secondary endosymbiotic events (as opposed to the primary, mitochondrial endosymbiosis). This biphasic model of evolution is substantially analogous to the scenario of the origin of universes in the eternal inflation version of modern cosmology. Under this model, universes like ours emerge in the infinite multiverse when the eternal process of exponential expansion, known as inflation, ceases in a particular region as a result of false vacuum decay, a first order phase transition process. The result is the nucleation of a new universe, which is traditionally denoted Big Bang, although this scenario is radically different from the Big Bang of the traditional model of an expanding universe. Hence I denote the phase transitions at the end of each inflationary epoch in the history of life Biological Big Bangs (BBB). Conclusion A Biological Big Bang (BBB) model is proposed for the major transitions in life's evolution. According to this model, each transition is a BBB such that new classes of biological entities emerge at the end of a rapid phase of evolution (inflation) that is characterized by extensive exchange of genetic information which takes distinct forms for different BBBs. The major types of new forms emerge independently, via a sampling process, from the pool of recombining entities of the preceding generation. This process is envisaged as being qualitatively different from tree-pattern cladogenesis. Reviewers This article was reviewed by William Martin, Sergei Maslov, and Leonid Mirny. PMID:17708768

43 CFR 426.5 - Ownership entitlement.

Code of Federal Regulations, 2010 CFR

2010-10-01

... one individual or a married couple, and for entities by the type of entity, as follows: (i) An... nonexempt land; (ii) Married couples who hold equal interests are entitled to receive irrigation water on a...

42 CFR 438.1 - Basis and scope.

Code of Federal Regulations, 2010 CFR

2010-10-01

... strategy; (v) Specifies certain prohibitions aimed at the prevention of fraud and abuse; (vi) Provides that... depending on the type of entity and on the authority under which the State contracts with the entity...

42 CFR 438.1 - Basis and scope.

Code of Federal Regulations, 2011 CFR

2011-10-01

... strategy; (v) Specifies certain prohibitions aimed at the prevention of fraud and abuse; (vi) Provides that... depending on the type of entity and on the authority under which the State contracts with the entity...

Deep learning with word embeddings improves biomedical named entity recognition.

PubMed

Habibi, Maryam; Weber, Leon; Neves, Mariana; Wiegandt, David Luis; Leser, Ulf

2017-07-15

Text mining has become an important tool for biomedical research. The most fundamental text-mining task is the recognition of biomedical named entities (NER), such as genes, chemicals and diseases. Current NER methods rely on pre-defined features which try to capture the specific surface properties of entity types, properties of the typical local context, background knowledge, and linguistic information. State-of-the-art tools are entity-specific, as dictionaries and empirically optimal feature sets differ between entity types, which makes their development costly. Furthermore, features are often optimized for a specific gold standard corpus, which makes extrapolation of quality measures difficult. We show that a completely generic method based on deep learning and statistical word embeddings [called long short-term memory network-conditional random field (LSTM-CRF)] outperforms state-of-the-art entity-specific NER tools, and often by a large margin. To this end, we compared the performance of LSTM-CRF on 33 data sets covering five different entity classes with that of best-of-class NER tools and an entity-agnostic CRF implementation. On average, F1-score of LSTM-CRF is 5% above that of the baselines, mostly due to a sharp increase in recall. The source code for LSTM-CRF is available at https://github.com/glample/tagger and the links to the corpora are available at https://corposaurus.github.io/corpora/ . habibima@informatik.hu-berlin.de. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com

Deep learning with word embeddings improves biomedical named entity recognition

PubMed Central

Habibi, Maryam; Weber, Leon; Neves, Mariana; Wiegandt, David Luis; Leser, Ulf

2017-01-01

Abstract Motivation: Text mining has become an important tool for biomedical research. The most fundamental text-mining task is the recognition of biomedical named entities (NER), such as genes, chemicals and diseases. Current NER methods rely on pre-defined features which try to capture the specific surface properties of entity types, properties of the typical local context, background knowledge, and linguistic information. State-of-the-art tools are entity-specific, as dictionaries and empirically optimal feature sets differ between entity types, which makes their development costly. Furthermore, features are often optimized for a specific gold standard corpus, which makes extrapolation of quality measures difficult. Results: We show that a completely generic method based on deep learning and statistical word embeddings [called long short-term memory network-conditional random field (LSTM-CRF)] outperforms state-of-the-art entity-specific NER tools, and often by a large margin. To this end, we compared the performance of LSTM-CRF on 33 data sets covering five different entity classes with that of best-of-class NER tools and an entity-agnostic CRF implementation. On average, F1-score of LSTM-CRF is 5% above that of the baselines, mostly due to a sharp increase in recall. Availability and implementation: The source code for LSTM-CRF is available at https://github.com/glample/tagger and the links to the corpora are available at https://corposaurus.github.io/corpora/. Contact: habibima@informatik.hu-berlin.de PMID:28881963

DDx: diagnostic assistance for the radiologist using PACS

NASA Astrophysics Data System (ADS)

Haynor, David R.

1993-09-01

A potentially valuable tool in medical imaging is the development, and integration with PACS, of systems which enhance the interpretive accuracy of the user -- his ability, given a set of findings (in the broad sense, including clinical information about the patient as well as characteristics of the lesion being analyzed), to assign the proper disease label, or diagnosis, to them. Such systems, which we call here interpretive tools (IT), contain a variety of types of information about diseases and their radiologic diagnosis. They can contain information about large numbers of diseases, including statistical information (incidence, characteristic anatomical locations, association with age and gender or with other diseases, probabilities of various findings given a disease), textual information (description of diseases, treatment, literature references, lists of other entities that might be confused with the disease of interest, additional diagnostic points that may not be represented, or even representable, within IT), and image-based information (typical and atypical examples for each entity and radiographic finding, examples of normal anatomy). These databases can be used both for teaching purposes and as a tool for improving interpretive accuracy [Swett, 1987]. This paper describes some of the requirements for these databases and then discusses early work on the implementation of DDx, an IT whose domain is neuroradiology.

Complaints against nursing homes: comparing two sources of complaint information and predictors of complaints.

PubMed

Troyer, Jennifer L; Sause, Wendy L

2011-08-01

Two consumer-derived measures of nursing home quality that have been underutilized by researchers are consumer complaints to the state certification agency between inspections and complaints to the Long-Term Care Ombudsman Program. This article describes these complaints, considers facility-level predictors of complaints, and examines how complaints to the 2 entities are related. This article uses North Carolina complaint data from the state certification agency and Ombudsman from 2002 to 2006. First, we outline the similarities and differences in the 2 complaint sources by considering descriptive statistics and examining the structure of the 2 agencies. Second, we examine the relationship between complaints and facility characteristics that have been predictive of traditional quality measures. Finally, we examine the relationships between the 2 types of complaints. We find that complaints to the 2 agencies exhibit distinct differences in substantiation rates, although the top complaint category for both agencies is quality of care. Having a higher proportion of Medicaid residents is generally not predictive of complaint volume, whereas having a higher proportion of Medicare residents is associated with higher complaint levels. We find a lack of association between complaints to the 2 agencies when examining specific matched categories of complaints in many cases, suggesting that the 2 entities are not duplicating efforts in these categories.

Multi-source and ontology-based retrieval engine for maize mutant phenotypes

USDA-ARS?s Scientific Manuscript database

In the midst of this genomics era, major plant genome databases are collecting massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc., as well as textual descriptions of many of these entities. While basic browsing and sear...

Linked Data for Software Security Concepts and Vulnerability Descriptions

DTIC Science & Technology

2013-07-01

named entity (NE) extractors such as DBpedia Spotlight, Alchemy API1, Extractiv2, OpenCalais3 and Zemanta were compared for their overall performance...presents substantial agreement for URI dis- ambiguation. Alchemy API, although preserving good performance in NE extraction and 1http://www.alchemyapi.com

7 CFR 353.8 - Accreditation of non-government facilities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... relationship to a larger corporate entity; and (iv) A description of the specific laboratory testing or... the facility is seeking accreditation must be identified and must possess the training, education, or... inspection services for which the facility seeks accreditation, and that training, education, or experience...

Primary disorders of the lymphatic vessels--a unified concept.

PubMed

Levine, C

1989-03-01

Congenital defects of lymphatics constitute a spectrum of disorders that may manifest with a variety of clinical presentations including lymphedema, chylous effusions, lymphangiomatous malformations with cystic masses and localized gigantism, and intestinal lymphangiectasia with malabsorption. These entities constitute a relatively rare group of disorders, the origin of which remains somewhat controversial, but in some it appears to be due to early lymphatic obstruction. Five cases are described, which demonstrate the anatomical pathology of these entities. A classification and description of the defects is also presented. An attempt is made to present a unified theory of origin for this seemingly diverse group of diseases. While these entities may be challenging from a diagnostic and therapeutic standpoint, a wide variety of imaging modalities, which includes lymphography, computed tomography scanning, and ultrasound, may be used to diagnose the extent and internal structural characteristics of the abnormalities.

Accommodating Ontologies to Biological Reality—Top-Level Categories of Cumulative-Constitutively Organized Material Entities

PubMed Central

Vogt, Lars; Grobe, Peter; Quast, Björn; Bartolomaeus, Thomas

2012-01-01

Background The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity. Methodology/Principal Findings Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for ‘portion of matter’ as another material building block. This implies the necessity for further extending BFO by ‘portion of matter’ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities. Conclusions/Significance We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material entity taxonomy. With these additions and the notion of granular representation, BFO would exhaustively cover all top-level types of material entities that application oriented ontologies may use as templates, while still maintaining the single inheritance principle. PMID:22253856

37 CFR 1.27 - Definition of small entities and establishing status as a small entity to permit payment of small...

Code of Federal Regulations, 2010 CFR

2010-07-01

... are required; fraud on the Office. 1.27 Section 1.27 Patents, Trademarks, and Copyrights UNITED STATES... and notification of loss of entitlement to small entity status are required; fraud on the Office. (a... country; (B) An organization of the type described in section 501(c)(3) of the Internal Revenue Code of...

Federally Created Entities: An Overview of Key Attributes. Report to the Ranking Member, Committee on Finance, U.S. Senate. GAO-10-97

ERIC Educational Resources Information Center

Ragland, Susan; Poling, Susan A.

2009-01-01

Over the years, Congress has created or authorized the creation of numerous entities to carry out federal programs and further public purposes. These federally created entities can be categorized into several types and serve a variety of missions. They are subject to varying governance, accountability, and transparency requirements through which…

Spatio-structural granularity of biological material entities

PubMed Central

2010-01-01

Background With the continuously increasing demands on knowledge- and data-management that databases have to meet, ontologies and the theories of granularity they use become more and more important. Unfortunately, currently used theories and schemes of granularity unnecessarily limit the performance of ontologies due to two shortcomings: (i) they do not allow the integration of multiple granularity perspectives into one granularity framework; (ii) they are not applicable to cumulative-constitutively organized material entities, which cover most of the biomedical material entities. Results The above mentioned shortcomings are responsible for the major inconsistencies in currently used spatio-structural granularity schemes. By using the Basic Formal Ontology (BFO) as a top-level ontology and Keet's general theory of granularity, a granularity framework is presented that is applicable to cumulative-constitutively organized material entities. It provides a scheme for granulating complex material entities into their constitutive and regional parts by integrating various compositional and spatial granularity perspectives. Within a scale dependent resolution perspective, it even allows distinguishing different types of representations of the same material entity. Within other scale dependent perspectives, which are based on specific types of measurements (e.g. weight, volume, etc.), the possibility of organizing instances of material entities independent of their parthood relations and only according to increasing measures is provided as well. All granularity perspectives are connected to one another through overcrossing granularity levels, together forming an integrated whole that uses the compositional object perspective as an integrating backbone. This granularity framework allows to consistently assign structural granularity values to all different types of material entities. Conclusions The here presented framework provides a spatio-structural granularity framework for all domain reference ontologies that model cumulative-constitutively organized material entities. With its multi-perspectives approach it allows querying an ontology stored in a database at one's own desired different levels of detail: The contents of a database can be organized according to diverse granularity perspectives, which in their turn provide different views on its content (i.e. data, knowledge), each organized into different levels of detail. PMID:20509878

14 CFR 291.44 - BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity.

Code of Federal Regulations, 2012 CFR

2012-01-01

... other than Jet A fuel, a footnote shall be added indicating the number of gallons and applicable costs... 14 Aeronautics and Space 4 2012-01-01 2012-01-01 false BTS Schedule P-12(a), Fuel Consumption by... TRANSPORTATION Reporting Rules § 291.44 BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity. (a...

14 CFR 291.44 - BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity.

Code of Federal Regulations, 2014 CFR

2014-01-01

... other than Jet A fuel, a footnote shall be added indicating the number of gallons and applicable costs... 14 Aeronautics and Space 4 2014-01-01 2014-01-01 false BTS Schedule P-12(a), Fuel Consumption by... TRANSPORTATION Reporting Rules § 291.44 BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity. (a...

14 CFR 291.44 - BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity.

Code of Federal Regulations, 2013 CFR

2013-01-01

... other than Jet A fuel, a footnote shall be added indicating the number of gallons and applicable costs... 14 Aeronautics and Space 4 2013-01-01 2013-01-01 false BTS Schedule P-12(a), Fuel Consumption by... TRANSPORTATION Reporting Rules § 291.44 BTS Schedule P-12(a), Fuel Consumption by Type of Service and Entity. (a...

Demographics of Head and Neck Cancer Patients: A Single Institution Experience

PubMed Central

Kitanova, Martina; Dzhenkov, Deyan L; Ghenev, Peter; Sapundzhiev, Nikolay

2017-01-01

Introduction Head and neck cancer (HNC) comprises a diverse group of oncological entities, originating from various tissue types and organ localizations, situated in the topographical regions of the head and neck (H&N). This single institution retrospective study was aimed at establishing the HNC patient demographics and categorizing the individual incidence of H&N malignancies, regarding their organ of origin and main histopathological type. Materials and methods All histologically verified cases of HNC from a single tertiary referral center were reviewed in a descriptive retrospective manner. Data sampling period was 47 months. Results Male to female ratio of the registered HNC cases was 3.24:1. The mean age of diagnosis was 63.84 ± 12.65 years, median 65 years. The most common HNC locations include the larynx 30.37% (n = 188), lips and oral cavity 29.08% (n = 180), pharynx 20.03% (n = 124) and salivary glands 10.94% (n = 68), with other locations such as the external nose, nasal cavity and sinuses and auricle and external ear canal harboring a minority of the cases. The main histopathological groups include squamous cell carcinoma 76.74% (n = 475) and adenocarcinoma 6.14% (n = 38), with other malignant entries such as other epithelial malignancies, primary tonsillar, mucosa-associated lymphoid tissue or parenchymal lymphomas, connective tissue neoplasias, neuroendocrine and vascular malignancies diagnosed in a minority of cases. Conclusion Considered to be relatively rare, HNC represents a diverse group of oncological entities with individual and specific demographic characteristics. The reported single institution results appear representative of the national incidence and characteristics of HNC. PMID:28875091

[Nonspecific interstitial pneumonitis: a clinicopathologic entity, histologic pattern or unclassified group of heterogeneous interstitial pneumonitis?].

PubMed

Morais, António; Moura, M Conceição Souto; Cruz, M Rosa; Gomes, Isabel

2004-01-01

Nonspecific interstitial pneumonitis (NSIP) initially described by Katzenstein and Fiorelli in 1994, seems to be a distinct clinicopathologic entity among idiopathic interstitial pneumonitis (IIP). Besides different histologic features from other IIP, NSIP is characterized by a better long-term outcome, associated with a better steroids responsiveness than idiopathic pulmonar fibrosis (IPF), where usually were included. Thus, differentiating NSIP from other IIP, namely IPF is very significant, since it has important therapeutic and prognostic implications. NSIP encloses different pathologies, namely those with inflammatory predominance (cellular subtype) or fibrous predominance (fibrosing subtype). NSIP is reviewed and discussed by the authors, after two clinical cases description.

Complex Landscape Terms in Seri

ERIC Educational Resources Information Center

O'Meara, Carolyn; Bohnemeyer, Jurgen

2008-01-01

The nominal lexicon of Seri is characterized by a prevalence of analytical descriptive terms. We explore the consequences of this typological trait in the landscape domain. The complex landscape terms of Seri classify geographic entities in terms of their material make-up and spatial properties such as shape, orientation, and merological…

76 FR 21325 - Notice of Funds Availability: Inviting Applications for the Market Access Program

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-15

... for the 2012 Market Access Program (MAP). The intended effect of this notice is to solicit... INFORMATION CONTACT: Entities wishing to apply for funding assistance should contact the Program Operations....gov/mos/programs/map.asp . SUPPLEMENTARY INFORMATION: I. Funding Opportunity Description Authority...

The Stereotype of the Indian in Adolescent Literature.

ERIC Educational Resources Information Center

Troy, Anne

Studies of teaching materials have shown that the American Indian has not been given fair representation in American history. Too often portrayed as inaccurate are such subjects as tribal entities and cultures, listings of current tribes and reservations, descriptions of languages and areas of occupation, foods, attire, and dates of historical…

Context and Structure in Automated Full-Text Information Access

DTIC Science & Technology

1994-04-29

Meisei, Makayo, Nitsuko and Tamura, all of Japan; Goldstar, Samsung and OPC of South Korea, and Sun Moon Star of Taiwan; AT&T says the practices have...IN MALAYSIA [ ... ] Another example topic description is shown below: Topic 034 <dom> Domain: Science and Technology <title>Topic: Entities Involved In

42 CFR 405.976 - Notice of a reconsideration.

Code of Federal Regulations, 2010 CFR

2010-10-01

... calculated to be understood by a beneficiary. (iii) The QIC must promptly notify the entity responsible for... to the parties' right to an ALJ hearing, including the applicable amount in controversy requirement... hearing is met when the reconsideration is partially or fully unfavorable; (8) A description of the...

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

PubMed

Blank, Carrine E; Cui, Hong; Moore, Lisa R; Walls, Ramona L

2016-01-01

MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. MicrO currently has ~14550 classes (~2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by ~24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we intend MicrO to be a powerful new tool to increase the computing power of bioinformatics tools such as the automated text mining of prokaryotic taxonomic descriptions using natural language processing. We also intend MicrO to support the development of new bioinformatics tools that aim to develop new connections between microbial phenotypes and genotypes (i.e., the gene content in genomes). Future ontology development will include incorporation of pathogenic phenotypes and prokaryotic habitats.

Automatically Recognizing Medication and Adverse Event Information From Food and Drug Administration’s Adverse Event Reporting System Narratives

PubMed Central

Polepalli Ramesh, Balaji; Belknap, Steven M; Li, Zuofeng; Frid, Nadya; West, Dennis P

2014-01-01

Background The Food and Drug Administration’s (FDA) Adverse Event Reporting System (FAERS) is a repository of spontaneously-reported adverse drug events (ADEs) for FDA-approved prescription drugs. FAERS reports include both structured reports and unstructured narratives. The narratives often include essential information for evaluation of the severity, causality, and description of ADEs that are not present in the structured data. The timely identification of unknown toxicities of prescription drugs is an important, unsolved problem. Objective The objective of this study was to develop an annotated corpus of FAERS narratives and biomedical named entity tagger to automatically identify ADE related information in the FAERS narratives. Methods We developed an annotation guideline and annotate medication information and adverse event related entities on 122 FAERS narratives comprising approximately 23,000 word tokens. A named entity tagger using supervised machine learning approaches was built for detecting medication information and adverse event entities using various categories of features. Results The annotated corpus had an agreement of over .9 Cohen’s kappa for medication and adverse event entities. The best performing tagger achieves an overall performance of 0.73 F1 score for detection of medication, adverse event and other named entities. Conclusions In this study, we developed an annotated corpus of FAERS narratives and machine learning based models for automatically extracting medication and adverse event information from the FAERS narratives. Our study is an important step towards enriching the FAERS data for postmarketing pharmacovigilance. PMID:25600332

Combined direct and indirect traumatic carotid-cavernous fistula (CCF): Case report and review of the literature.

PubMed

Abecassis, Isaac Josh; Morton, Ryan P; Kim, Louis J; Ghodke, Basavaraj V; Levitt, Michael R

2017-10-01

Within the current Barrow classification system, there are no categorical descriptions or reports in the literature of cavernous carotid fistulas (CCFs) with both a direct component (type A) and separate indirect contribution (type B, C, or D). We report the first definitive case of a combined simultaneous traumatic direct and indirect CCF, and review the literature on the similar existing entity of traumatic indirect CCFs presenting delayed and subsequent to the treatment of traumatic, direct CCFs. We report a case of simultaneous direct type A CCF with a traumatic indirect CCF component and a review of the relevant literature. An 18year-old female presented after a motor vehicle collision. A diagnostic cerebral angiogram confirmed the diagnosis of CCF, with contribution both directly from the ICA and indirectly via branches of the ECA. The direct component of the CCF was first treated in 3 stages via both transarterial and transvenous coil embolization, followed by a final 4th stage of parent vessel sacrifice in order to treat the residual direct component, with transarterial embolization to treat residual indirect CCF activity. To our knowledge, this is the first report of a traumatic CCF with simultaneous direct (type A) and indirect via the ECA (type C) contributions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Inflammatory myoglandular polyp--a rare but distinct type of colorectal polyps.

PubMed

Becheanu, Gabriel; Stamm, Bernhard

2003-01-01

The aim of this paper was to report another example of a rare type of colorectal polyps, the inflammatory myoglandular polyp, and to reaffirm this type of polyp as a distinct entity. This solitary pedunculated polyp was detected after a single episode of rectal bleeding. It was situated in the sigmoid colon, measured 2.5 cm in greatest diameter, and was composed almost exclusively of smooth muscles and hyperplastic glands. The patient had neither chronic colitis nor diverticula. Clinical presentation, localization, and histology give this type of polyp a unique appearance and justify its designation as a separate entity.

Necrotizing and eosinophilic masticatory myositis in farmed mink: a preliminary description.

PubMed

Needle, D B; Hollinger, C; Shelton, G D; Fitzgerald, S D

2014-01-01

This report describes necrotizing and eosinophilic myositis affecting the masticatory muscles of a group of mink. Affected animals demonstrated sudden death with marked subcutaneous oedema over the dorsal head. The temporalis and masseter muscles were pale, swollen and friable. Histologic changes consisted of varying degrees of myodegeneration, myonecrosis and inflammation. Eosinophils were prominent in the inflammatory infiltrate. Similar to dogs, masticatory muscles in mink were found to contain unique type 2M fibres, suggesting a possible target for an immune response. Aerobic and anaerobic tissue cultures of the affected musculature revealed no significant pathogens. Histological and nutritional analyses were not typical of vitamin E/selenium deficiency. This case series supports the existence of a novel disease entity in mink with some features comparable with masticatory muscle myositis in dogs. Copyright © 2014 Elsevier Ltd. All rights reserved.

A brief history of typical absence seizures - Petit mal revisited.

PubMed

Brigo, Francesco; Trinka, Eugen; Lattanzi, Simona; Bragazzi, Nicola Luigi; Nardone, Raffaele; Martini, Mariano

2018-03-01

In this article, we have traced back the history of typical absence seizures, from their initial clinical description to the more recent nosological position. The first description of absence seizures was made by Poupart in 1705 and Tissot in 1770. In 1824, Calmeil introduced the term "absences", and in 1838, Esquirol for the first time used the term petit mal. Reynolds instead used the term "epilepsia mitior" (milder epilepsy) and provided a comprehensive description of absence seizures (1861). In 1854, Delasiauve ranked absences as the seizure type with lower severity and introduced the concept of idiopathic epilepsy. Otto Binswanger (1899) discussed the role of cortex in the pathophysiology of "abortive seizures", whereas William Gowers (1901) emphasized the importance of a detailed clinical history to identify nonmotor seizures or very mild motor phenomena which otherwise may go unnoticed or considered not epileptic. At the beginning of the 20th Century, the term pyknolepsy was introduced, but initially was not universally considered as a type of epilepsy; it was definitely recognized as an epileptic entity only in 1945, based on electroencephalogram (EEG) recordings. Hans Berger, the inventor of the EEG, made also the first EEG recording of an atypical absence (his results were published only in 1933), whereas the characteristic EEG pattern was reported by neurophysiologists of the Harvard Medical School in 1935. The discovery of EEG made it also possible to differentiate absence seizures from so called "psychomotor" seizures occurring in temporal lobe epilepsy. Penfield and Jasper (1938) considered absences as expression of "centrencephalic epilepsy". Typical absences seizures are now classified by the International League Against Epilepsy among generalized nonmotor (absence) seizures. Copyright © 2018 Elsevier Inc. All rights reserved.

Storybooks aren't just for fun: narrative and non-narrative picture books foster equal amounts of generic language during mother-toddler book sharing

PubMed Central

Nyhout, Angela; O'Neill, Daniela K.

2014-01-01

Parents and children encounter a variety of animals and objects in the early picture books they share, but little is known about how the context in which these entities are presented influences talk about them. The present study investigated how the presence or absence of a visual narrative context influences mothers' tendency to refer to animals as individual characters or as members of a kind when sharing picture books with their toddlers (mean age 21.3 months). Mother-child dyads shared both a narrative and a non-narrative book, each featuring six animals and matched in terms of length and quantity of text. Mothers made more specific (individual-referring) statements about animals in the narrative books, whereas they provided more labels for animals in the non-narrative books. But, of most interest, the frequency and proportion of mothers' use of generic (kind-referring) utterances did not differ across the two different types of books. Further coding of the content of the utterances revealed that mothers provided more story-specific descriptions of states and actions of the animals when sharing narrative books and more physical descriptions of animals when sharing non-narrative books. However, the two books did not differ in terms of their elicitation of natural facts about the animals. Overall, although the two types of books encouraged different types of talk from mothers, they stimulated generic language and talk about natural facts to an equal degree. Implications for learning from picture storybooks and book genre selection in classrooms and home reading are discussed. PMID:24795675

Storybooks aren't just for fun: narrative and non-narrative picture books foster equal amounts of generic language during mother-toddler book sharing.

PubMed

Nyhout, Angela; O'Neill, Daniela K

2014-01-01

Parents and children encounter a variety of animals and objects in the early picture books they share, but little is known about how the context in which these entities are presented influences talk about them. The present study investigated how the presence or absence of a visual narrative context influences mothers' tendency to refer to animals as individual characters or as members of a kind when sharing picture books with their toddlers (mean age 21.3 months). Mother-child dyads shared both a narrative and a non-narrative book, each featuring six animals and matched in terms of length and quantity of text. Mothers made more specific (individual-referring) statements about animals in the narrative books, whereas they provided more labels for animals in the non-narrative books. But, of most interest, the frequency and proportion of mothers' use of generic (kind-referring) utterances did not differ across the two different types of books. Further coding of the content of the utterances revealed that mothers provided more story-specific descriptions of states and actions of the animals when sharing narrative books and more physical descriptions of animals when sharing non-narrative books. However, the two books did not differ in terms of their elicitation of natural facts about the animals. Overall, although the two types of books encouraged different types of talk from mothers, they stimulated generic language and talk about natural facts to an equal degree. Implications for learning from picture storybooks and book genre selection in classrooms and home reading are discussed.

Computed tomography of congenital brain malformations

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

Sarwar, M.

1984-01-01

This book is illustrated showing each condition. This book is designed to correlate the pathology of CNS malformations with their CT scan appearance, mainly on the axial images. The author has drawn upon his personal experience and the information gleaned from the literature dealing with the description of the CT scan findings of these malformations. The emphasis is on simplicity of description. Since a large degree of morphological variation exists in each entity, numerous illustrations (wherever applicable) are shown to depict those variations. When appropriate, deficiency of the CT scan in the evaluation of these CNS malformations also is indicated.more » A description of CNS embryology is included as well.« less

Metrology in health: a pilot study

NASA Astrophysics Data System (ADS)

Ferreira, M.; Matos, A.

2015-02-01

The purpose of this paper is to identify and analyze some relevant issues which arise when the concept of metrological traceability is applied to health care facilities. Discussion is structured around the results that were obtained through a characterization and comparative description of the practices applied in 45 different Portuguese health entities. Following a qualitative exploratory approach, the information collected was the support for the initial research hypotheses and the development of the questionnaire survey. It was also applied a quantitative methodology that included a descriptive and inferential statistical analysis of the experimental data set.

TaggerOne: joint named entity recognition and normalization with semi-Markov Models

PubMed Central

Leaman, Robert; Lu, Zhiyong

2016-01-01

Motivation: Text mining is increasingly used to manage the accelerating pace of the biomedical literature. Many text mining applications depend on accurate named entity recognition (NER) and normalization (grounding). While high performing machine learning methods trainable for many entity types exist for NER, normalization methods are usually specialized to a single entity type. NER and normalization systems are also typically used in a serial pipeline, causing cascading errors and limiting the ability of the NER system to directly exploit the lexical information provided by the normalization. Methods: We propose the first machine learning model for joint NER and normalization during both training and prediction. The model is trainable for arbitrary entity types and consists of a semi-Markov structured linear classifier, with a rich feature approach for NER and supervised semantic indexing for normalization. We also introduce TaggerOne, a Java implementation of our model as a general toolkit for joint NER and normalization. TaggerOne is not specific to any entity type, requiring only annotated training data and a corresponding lexicon, and has been optimized for high throughput. Results: We validated TaggerOne with multiple gold-standard corpora containing both mention- and concept-level annotations. Benchmarking results show that TaggerOne achieves high performance on diseases (NCBI Disease corpus, NER f-score: 0.829, normalization f-score: 0.807) and chemicals (BioCreative 5 CDR corpus, NER f-score: 0.914, normalization f-score 0.895). These results compare favorably to the previous state of the art, notwithstanding the greater flexibility of the model. We conclude that jointly modeling NER and normalization greatly improves performance. Availability and Implementation: The TaggerOne source code and an online demonstration are available at: http://www.ncbi.nlm.nih.gov/bionlp/taggerone Contact: zhiyong.lu@nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27283952

TaggerOne: joint named entity recognition and normalization with semi-Markov Models.

PubMed

Leaman, Robert; Lu, Zhiyong

2016-09-15

Text mining is increasingly used to manage the accelerating pace of the biomedical literature. Many text mining applications depend on accurate named entity recognition (NER) and normalization (grounding). While high performing machine learning methods trainable for many entity types exist for NER, normalization methods are usually specialized to a single entity type. NER and normalization systems are also typically used in a serial pipeline, causing cascading errors and limiting the ability of the NER system to directly exploit the lexical information provided by the normalization. We propose the first machine learning model for joint NER and normalization during both training and prediction. The model is trainable for arbitrary entity types and consists of a semi-Markov structured linear classifier, with a rich feature approach for NER and supervised semantic indexing for normalization. We also introduce TaggerOne, a Java implementation of our model as a general toolkit for joint NER and normalization. TaggerOne is not specific to any entity type, requiring only annotated training data and a corresponding lexicon, and has been optimized for high throughput. We validated TaggerOne with multiple gold-standard corpora containing both mention- and concept-level annotations. Benchmarking results show that TaggerOne achieves high performance on diseases (NCBI Disease corpus, NER f-score: 0.829, normalization f-score: 0.807) and chemicals (BioCreative 5 CDR corpus, NER f-score: 0.914, normalization f-score 0.895). These results compare favorably to the previous state of the art, notwithstanding the greater flexibility of the model. We conclude that jointly modeling NER and normalization greatly improves performance. The TaggerOne source code and an online demonstration are available at: http://www.ncbi.nlm.nih.gov/bionlp/taggerone zhiyong.lu@nih.gov Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the US.

45 CFR 2517.400 - What must a State Commission or grantmaking entity include in an application for a grant?

Code of Federal Regulations, 2010 CFR

2010-10-01

...-LEARNING PROGRAMS Application Contents § 2517.400 What must a State Commission or grantmaking entity... promoting service-learning through programs under this part. The plan must describe the types of community...

45 CFR 2517.400 - What must a State Commission or grantmaking entity include in an application for a grant?

Code of Federal Regulations, 2011 CFR

2011-10-01

...-LEARNING PROGRAMS Application Contents § 2517.400 What must a State Commission or grantmaking entity... promoting service-learning through programs under this part. The plan must describe the types of community...

78 FR 12006 - Wireline Competition Bureau Seeks Comment on Connect America Phase II Support for Price Cap Areas...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-21

... requirements be modified for carriers receiving frozen support? What measures would need to be in place to... certifications or local OVS franchises. The Commission does not have financial or employment information.... Description of Projected Reporting, Recordkeeping, and Other Compliance Requirements for Small Entities 31. In...

Tuberculous peritonitis: CT appearance

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

Hanson, R.D.; Hunter, T.B.

1985-05-01

Rare, sporadic cases of tuberculous peritonitis do occur in the United States and other advanced countries. Because there are few descriptions of the CT appearance of the peritoneal forms of tuberculous (TB), this report illustrates a case of tuberculous peritonitis with prominent CT findings and discusses the differentiation of this entity from other, more common diseases.

78 FR 11809 - Fisheries of the Northeastern United States; Atlantic Bluefish Fishery; 2013-2014 Atlantic...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-20

..., economic, and social impacts of the recommendations. NMFS is responsible for reviewing these... describes the economic impact this proposed rule, if adopted, would have on small entities. A description of... available from the Council (see ADDRESSES). Small businesses operating in commercial and recreational (i.e...

77 FR 51540 - Medicare Program; Approved Renewal of Deeming Authority of the Accreditation Association for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-24

... Provider Organizations for a term of 6 years. DATES: This final notice is effective through July 10, 2018... financially affiliated with the entity being surveyed. A description of the organization's data management and... Health Care, Inc. for Medicare Advantage Health Maintenance Organizations and Local Preferred Provider...

Perspective-Shifts in Event Descriptions in Tamil Child Language

ERIC Educational Resources Information Center

Narasimhan, Bhuvana; Gullberg, Marianne

2006-01-01

Children are able to take multiple perspectives in talking about entities and events. But the nature of children's sensitivities to the complex patterns of perspective-taking in adult language is unknown. We examine perspective-taking in four- and six-year-old Tamil-speaking children describing placement events, as reflected in the use of a…

World Perspective Case Descriptions on Educational Programs for Adults: Czechoslovakia.

ERIC Educational Resources Information Center

Skoda, Kamil; Hartl, Pavel

This document contains two case studies of Czechoslovakian adult education: (1) Czechoslovakian Adult Education (Skoda) and (2) the House of Culture and Its Function in Adult Education (Hartl). Each study begins with a "face sheet" on which is recorded basic information about the entity studied and the case study itself. About half of…

World Perspective Case Descriptions on Educational Programs for Adults: Argentina.

ERIC Educational Resources Information Center

Hernandez, Isabel

This document consists of two case studies of adult education in Argentina: (1) Adult Education--Governmental and Nongovernmental Action in Latin America and (2) Education and the Elderly Population in Argentina. Each study begins with a "face sheet" on which is recorded basic information about the entity studied and the case study…

42 CFR 23.4 - How must an entity apply for assignment?

Code of Federal Regulations, 2010 CFR

2010-10-01

... applicant's overall organizational structure; (2) A justification of the request for the assignment of personnel based upon the needs of the health manpower shortage area; (3) A description of the applicant's..., equipment and supplies; (4) A list of the proposed fees and discounted fees to be charged for the provision...

On the Role of Mathematics in Physics

ERIC Educational Resources Information Center

Quale, Andreas

2011-01-01

I examine the association between the observable physical world and the mathematical models of theoretical physics. These models will exhibit many entities that have no counterpart in the physical world, but which are still necessary for the mathematical description of physical systems. Moreover, when the model is applied to the analysis of a…

Characterizing autopoiesis in the game of life.

PubMed

Beer, Randall D

2015-01-01

Maturana and Varela's concept of autopoiesis defines the essential organization of living systems and serves as a foundation for their biology of cognition and the enactive approach to cognitive science. As an initial step toward a more formal analysis of autopoiesis, this article investigates its application to the compact, recurrent spatiotemporal patterns that arise in Conway's Game-of-Life cellular automaton. In particular, we demonstrate how such entities can be formulated as self-constructing networks of interdependent processes that maintain their own boundaries. We then characterize the specific organizations of several such entities, suggest a way to simplify the descriptions of these organizations, and briefly consider the transformation of such organizations over time.

Question analysis for Indonesian comparative question

NASA Astrophysics Data System (ADS)

Saelan, A.; Purwarianti, A.; Widyantoro, D. H.

2017-01-01

Information seeking is one of human needs today. Comparing things using search engine surely take more times than search only one thing. In this paper, we analyzed comparative questions for comparative question answering system. Comparative question is a question that comparing two or more entities. We grouped comparative questions into 5 types: selection between mentioned entities, selection between unmentioned entities, selection between any entity, comparison, and yes or no question. Then we extracted 4 types of information from comparative questions: entity, aspect, comparison, and constraint. We built classifiers for classification task and information extraction task. Features used for classification task are bag of words, whether for information extraction, we used lexical, 2 previous and following words lexical, and previous label as features. We tried 2 scenarios: classification first and extraction first. For classification first, we used classification result as a feature for extraction. Otherwise, for extraction first, we used extraction result as features for classification. We found that the result would be better if we do extraction first before classification. For the extraction task, classification using SMO gave the best result (88.78%), while for classification, it is better to use naïve bayes (82.35%).

Identifying interactions between chemical entities in biomedical text.

PubMed

Lamurias, Andre; Ferreira, João D; Couto, Francisco M

2014-10-23

Interactions between chemical compounds described in biomedical text can be of great importance to drug discovery and design, as well as pharmacovigilance. We developed a novel system, \\"Identifying Interactions between Chemical Entities\\" (IICE), to identify chemical interactions described in text. Kernel-based Support Vector Machines first identify the interactions and then an ensemble classifier validates and classifies the type of each interaction. This relation extraction module was evaluated with the corpus released for the DDI Extraction task of SemEval 2013, obtaining results comparable to state-of-the-art methods for this type of task. We integrated this module with our chemical named entity recognition module and made the whole system available as a web tool at www.lasige.di.fc.ul.pt/webtools/iice.

Identifying interactions between chemical entities in biomedical text.

PubMed

Lamurias, Andre; Ferreira, João D; Couto, Francisco M

2014-12-01

Interactions between chemical compounds described in biomedical text can be of great importance to drug discovery and design, as well as pharmacovigilance. We developed a novel system, "Identifying Interactions between Chemical Entities" (IICE), to identify chemical interactions described in text. Kernel-based Support Vector Machines first identify the interactions and then an ensemble classifier validates and classifies the type of each interaction. This relation extraction module was evaluated with the corpus released for the DDI Extraction task of SemEval 2013, obtaining results comparable to stateof- the-art methods for this type of task. We integrated this module with our chemical named entity recognition module and made the whole system available as a web tool at www.lasige.di.fc.ul.pt/webtools/iice.

42 CFR 422.2274 - Broker and agent requirements.

Code of Federal Regulations, 2010 CFR

2010-10-01

... (CONTINUED) MEDICARE PROGRAM MEDICARE ADVANTAGE PROGRAM Medicare Advantage Marketing Requirements § 422.2274... with a third party entity such as a Field Marketing Organization or similar type entity to sell its insurance products, or perform services (for example, training, customer service, or agent recruitment), the...

Representing Medical Knowledge in the Form of Structured Text: The Development of Current Disease Descriptions*

PubMed Central

Nelson, Stuart J.; Sherertz, David D.; Erlbaum, Mark S.; Tuttle, Mark S.

1989-01-01

As part of the Unified Medical Language System (UMLS) initiative, some 900 diseases have been described using “structured text.” Structured text is words and short phrases entered under labelled contexts. Vocabulary is not controlled. The contexts comprise a template for the disease description. The structured text is both manipulable by machine and readable by humans. Use of the template was natural, and only a few problems arose in using the template. Instructions to disease description composers must be explicit in definitions of the contexts. Diseases to be described are chosen, after clustering related diseases, according to the distinctions that physicians practicing in the area under question believe are important. Limiting disease descriptions to primitive observations and to entities otherwise described within the corpus appears to be both feasible and desirable.

Triple-negative breast cancer: the importance of molecular and histologic subtyping, and recognition of low-grade variants.

PubMed

Pareja, Fresia; Geyer, Felipe C; Marchiò, Caterina; Burke, Kathleen A; Weigelt, Britta; Reis-Filho, Jorge S

2016-01-01

Triple-negative breast cancers (TNBCs), defined by lack of expression of estrogen receptor, progesterone receptor and HER2, account for 12-17% of breast cancers and are clinically perceived as a discrete breast cancer subgroup. Nonetheless, TNBC has been shown to constitute a vastly heterogeneous disease encompassing a wide spectrum of entities with marked genetic, transcriptional, histological and clinical differences. Although most TNBCs are high-grade tumors, there are well-characterized low-grade TNBCs that have an indolent clinical course, whose natural history, molecular features and optimal therapy vastly differ from those of high-grade TNBCs. Secretory and adenoid cystic carcinomas are two histologic types of TNBCs underpinned by specific fusion genes; these tumors have an indolent clinical behavior and lack all of the cardinal molecular features of high-grade triple-negative disease. Recent studies of rare entities, including lesions once believed to constitute mere benign breast disease (e.g., microglandular adenosis), have resulted in the identification of potential precursors of TNBC and suggested the existence of a family of low-grade triple-negative lesions that, despite having low-grade morphology and indolent clinical behavior, have been shown to harbor the complex genomic landscape of common forms of TNBC, and may progress to high-grade disease. In this review, we describe the heterogeneity of TNBC and focus on the histologic and molecular features of low-grade forms of TNBC. Germane to addressing the challenges posed by the so-called triple-negative disease is the realization that TNBC is merely a descriptive term, and that low-grade types of TNBC may be driven by distinct sets of genetic alterations.

Triple-negative breast cancer: the importance of molecular and histologic subtyping, and recognition of low-grade variants

PubMed Central

Pareja, Fresia; Geyer, Felipe C; Marchiò, Caterina; Burke, Kathleen A; Weigelt, Britta; Reis-Filho, Jorge S

2016-01-01

Triple-negative breast cancers (TNBCs), defined by lack of expression of estrogen receptor, progesterone receptor and HER2, account for 12–17% of breast cancers and are clinically perceived as a discrete breast cancer subgroup. Nonetheless, TNBC has been shown to constitute a vastly heterogeneous disease encompassing a wide spectrum of entities with marked genetic, transcriptional, histological and clinical differences. Although most TNBCs are high-grade tumors, there are well-characterized low-grade TNBCs that have an indolent clinical course, whose natural history, molecular features and optimal therapy vastly differ from those of high-grade TNBCs. Secretory and adenoid cystic carcinomas are two histologic types of TNBCs underpinned by specific fusion genes; these tumors have an indolent clinical behavior and lack all of the cardinal molecular features of high-grade triple-negative disease. Recent studies of rare entities, including lesions once believed to constitute mere benign breast disease (e.g., microglandular adenosis), have resulted in the identification of potential precursors of TNBC and suggested the existence of a family of low-grade triple-negative lesions that, despite having low-grade morphology and indolent clinical behavior, have been shown to harbor the complex genomic landscape of common forms of TNBC, and may progress to high-grade disease. In this review, we describe the heterogeneity of TNBC and focus on the histologic and molecular features of low-grade forms of TNBC. Germane to addressing the challenges posed by the so-called triple-negative disease is the realization that TNBC is merely a descriptive term, and that low-grade types of TNBC may be driven by distinct sets of genetic alterations. PMID:28721389

Valuation of imaging centers: alternative methods and detailed description of the discounted cash flow approach.

PubMed

Russell, Philip J

2007-01-01

Medical imaging centers are an increasingly integral part of the medical services landscape in America. There are many instances in which owners and potential buyers of these enterprises want to ascertain the value of the businesses. There is an industry of professionals who provide expert valuation services for many types of businesses using various recognized alternative methods, some of which are more appropriate than others when valuing an imaging center. The federal government has prescribed parameters for all valuations if they lead to transactions in which fair market value is mandated, and it also expects transactions to adhere to more generalized laws relating to entities that provide services to Medicare patients. Radiologists who own, or who are contemplating ownership of, imaging center operations need to understand the principles of valuation, specifically the factors that are involved in a discounted cash flow determination of fair market value.

Regulatory Forum Opinion Piece*: Dispelling Confusing Pathology Terminology: Recognition and Interpretation of Selected Rodent Renal Tubule Lesions.

PubMed

Seely, John Curtis; Frazier, Kendall S

2015-06-01

Renal tubule lesions often prove troublesome for toxicologic pathologists because of the diverse nature and interrelated cell types within the kidney and the presence of spontaneous lesions with overlapping morphologies similar to those induced by renal toxicants. Although there are a number of guidance documents available citing straightforward diagnostic criteria of tubule lesions for the pathologist to refer to, most are presented without further advice on the when to or to the why and the why not of diagnosing one lesion over another. Documents presenting diagnostic perspectives and recommendations derived from an author's experience are limited since guidance documents are generally based on descriptive observations. In this Regulatory Forum opinion piece, the authors attempt to dispel confusing renal tubule lesion terminology in laboratory animal species by suggesting histological advice on the recognition and interpretation of these complex entities. © 2015 by The Author(s).

OWL references in ORM conceptual modelling

NASA Astrophysics Data System (ADS)

Matula, Jiri; Belunek, Roman; Hunka, Frantisek

2017-07-01

Object Role Modelling methodology is the fact-based type of conceptual modelling. The aim of the paper is to emphasize a close connection to OWL documents and its possible mutual cooperation. The definition of entities or domain values is an indispensable part of the conceptual schema design procedure defined by the ORM methodology. Many of these entities are already defined in OWL documents. Therefore, it is not necessary to declare entities again, whereas it is possible to utilize references from OWL documents during modelling of information systems.

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

Newman, J.R.; Maltby, J.H.

The purpose of this presentation was to discuss the emerging role of financial entities in determining environmental requirements for international power projects. The paper outlines the following: emerging conditions; examples of announced privatization energy projects by country; types of government and international financial entity sources; problems for IPPs; similarity and differences between the World Bank and the USEPA; comparison of the international standards and regulations for power plants; recent trends/issues involving international power project approval; and recommendations for understanding/expediting the financial entities` environmental approval process and how to expedite this process.

Mining semantic networks of bioinformatics e-resources from the literature

PubMed Central

2011-01-01

Background There have been a number of recent efforts (e.g. BioCatalogue, BioMoby) to systematically catalogue bioinformatics tools, services and datasets. These efforts rely on manual curation, making it difficult to cope with the huge influx of various electronic resources that have been provided by the bioinformatics community. We present a text mining approach that utilises the literature to automatically extract descriptions and semantically profile bioinformatics resources to make them available for resource discovery and exploration through semantic networks that contain related resources. Results The method identifies the mentions of resources in the literature and assigns a set of co-occurring terminological entities (descriptors) to represent them. We have processed 2,691 full-text bioinformatics articles and extracted profiles of 12,452 resources containing associated descriptors with binary and tf*idf weights. Since such representations are typically sparse (on average 13.77 features per resource), we used lexical kernel metrics to identify semantically related resources via descriptor smoothing. Resources are then clustered or linked into semantic networks, providing the users (bioinformaticians, curators and service/tool crawlers) with a possibility to explore algorithms, tools, services and datasets based on their relatedness. Manual exploration of links between a set of 18 well-known bioinformatics resources suggests that the method was able to identify and group semantically related entities. Conclusions The results have shown that the method can reconstruct interesting functional links between resources (e.g. linking data types and algorithms), in particular when tf*idf-like weights are used for profiling. This demonstrates the potential of combining literature mining and simple lexical kernel methods to model relatedness between resource descriptors in particular when there are few features, thus potentially improving the resource description, discovery and exploration process. The resource profiles are available at http://gnode1.mib.man.ac.uk/bioinf/semnets.html PMID:21388573

Determinants of Non-Compliance of Public Procurement Regulations in Kenyan Secondary Schools

ERIC Educational Resources Information Center

Migosi, Joash; Ombuki, Charles; Ombuki, Kennedy N.; Evusa, Zablon

2013-01-01

Kenya's public procurement and disposal Act of 2005 sets out clear rules and procedures for public procurement entities to follow; however this does not seem to be the case. This study sought to examine determinants of Non-compliance to the Public Procurement Regulations in Kenyan Secondary Schools. The study adopted a descriptive survey research.…

A Walking Contradiction, Partly Truth and Partly Fiction: A Critique of Stoesz' The Child Welfare Cartel

ERIC Educational Resources Information Center

Ellett, Alberta J.

2016-01-01

This article is a critique of David Stoesz' descriptions of organizational issues in child welfare, and more specifically, the relationships between the U.S. Children's Bureau and the National Child Welfare Workforce Institute. The focus is on Stoesz perspectives and assessments of sub-entities (cartels) that are currently influencing funding and…

75 FR 8968 - Draft Guidance for Industry on Adaptive Design Clinical Trials for Drugs and Biologics; Availability

Federal Register 2010, 2011, 2012, 2013, 2014

2010-02-26

... the drug development process, it is particularly important to protect study blinding of an adaptive...) and including a description of the responsibilities of each entity involved in the process. Based on... that each SOP will take approximately 30 minutes to document and maintain. B. Perform Simulations and...

10 CFR 900.5 - Request for coordination.

Code of Federal Regulations, 2010 CFR

2010-01-01

..., including: (i) The voltage and type of current (alternating or direct); (ii) The length of the transmission... contact information at all permitting entities and all non-Federal entities. (c) The written request for coordination may be filed by mail or hand delivery with the Director at 1000 Independence Avenue, SW...

77 FR 12205 - Mevinphos; Order Revoking Tolerances

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-29

... readers regarding entities likely to be affected by this action. Other types of entities not listed in... commodities listed in the regulatory text of this document that are treated with the pesticide subject to this... Executive Orders 13132, and 13175 This order directly regulates growers, food processors, food handlers and...

50 CFR 679.81 - Rockfish Program annual harvester and processor privileges.

Code of Federal Regulations, 2010 CFR

2010-10-01

... legal name; the type of business entity under which the rockfish cooperative is organized; the state in which the rockfish cooperative is legally registered as a business entity; Tax ID number, date of incorporation, the printed name of the rockfish cooperative's designated representative; the permanent business...

78 FR 5565 - Modifications to the HIPAA Privacy, Security, Enforcement, and Breach Notification Rules Under...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-01-25

... certain health information, such as standards for certain health care transactions conducted electronically and code sets and unique identifiers for health care providers and employers. The HIPAA... HIPAA apply to three types of entities, which are known as ``covered entities'': health care providers...

77 FR 42433 - Difenoconazole; Pesticide Tolerances

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-19

... INFORMATION: I. General Information A. Does this action apply to me? You may be potentially affected by this... affected entities may include, but are not limited to those engaged in the following activities: Crop... provide a guide for readers regarding entities likely to be affected by this action. Other types of...

76 FR 43874 - Privacy of Consumer Financial Information; Conforming Amendments Under Dodd-Frank Act

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-22

... pool operators (``CPOs''), and introducing brokers (``IBs''). The scope of the part 160 rules mirrors... respect to those Commission-regulated entities that were previously complying with part 160--FCMs, IBs... regulations currently applies to several types of Commission-regulated entities, including FCMs, IBs, CTAs...

CKD in diabetes: diabetic kidney disease versus nondiabetic kidney disease.

PubMed

Anders, Hans-Joachim; Huber, Tobias B; Isermann, Berend; Schiffer, Mario

2018-06-01

The increasing global prevalence of type 2 diabetes mellitus (T2DM) and chronic kidney disease (CKD) has prompted research efforts to tackle the growing epidemic of diabetic kidney disease (DKD; also known as diabetic nephropathy). The limited success of much of this research might in part be due to the fact that not all patients diagnosed with DKD have renal dysfunction as a consequence of their diabetes mellitus. Patients who present with CKD and diabetes mellitus (type 1 or type 2) can have true DKD (wherein CKD is a direct consequence of their diabetes status), nondiabetic kidney disease (NDKD) coincident with diabetes mellitus, or a combination of both DKD and NDKD. Preclinical studies using models that more accurately mimic these three entities might improve the ability of animal models to predict clinical trial outcomes. Moreover, improved insights into the pathomechanisms that are shared by these entities - including sodium-glucose cotransporter 2 (SGLT2) and renin-angiotensin system-driven glomerular hyperfiltration and tubular hyper-reabsorption - as well as those that are unique to individual entities might lead to the identification of new treatment targets. Acknowledging that the clinical entity of CKD plus diabetes mellitus encompasses NDKD as well as DKD could help solve some of the urgent unmet medical needs of patients affected by these conditions.

Two rare entities in the same palate lesion: hyalinizing-type clear cell carcinoma and necrotizing sialometaplasia.

PubMed

Arpaci, Rabia Bozdoğan; Kara, Tuba; Porgali, Canan; Serinsoz, Ebru; Polat, Ayse; Vayisoglu, Yusuf; Ozcan, Cengiz

2014-05-01

Hyalinizing clear cell carcinoma is a low-grade malignant epithelial neoplasm of the salivary glands. The tumor has epithelial cells and lacks myoepithelial cells. Necrotizing sialometaplasia is a benign, self-limiting lesion of the salivary glands. The clinical and histologic features mimic those of mucoepidermoid carcinoma or squamous cell carcinoma. The importance of these entities are the rarity of both of them and their potential to be misdiagnosed as other lesions. Pathologists and clinicians should be aware of these entities to prevent misdiagnosis. This is the first clinical report of 2 rare and consecutive different entities of the same location on the hard palate to our knowledge.

Reporting of dental status from full-arch radiographs: Descriptive analysis and methodological aspects.

PubMed

Huettig, Fabian; Axmann, Detlef

2014-10-16

To identify standards, how entities of dental status are assessed and reported from full-arch radiographs of adults. A PubMed (Medline) search was performed in November 2011. Literature had to report at least one out of four defined entities using radiographs: number of teeth or implants; caries, fillings or restorations; root-canal fillings and apical health; alveolar bone level. Cohorts included to the study had to be of adult age. Methods of radiographic assessment were noted and checked for the later mode of report in text, tables or diagrams. For comparability, the encountered mode of report was operationalized to a logical expression. Thirty-seven out of 199 articles were evaluated via full-text review. Only one article reported all four entities. Eight articles reported at the maximum 3 comparable entities. However, comparability is impeded because of the usage of absolute or relative frequency, mean or median values as well as grouping. Furthermore the methods of assessment were different or not described sufficiently. Consequently, established sum scores turned out to be highly questionable, too. The amount of missing data within all studies remained unclear. It is even so remissed to mention supernumerary and aplased teeth as well as the count of third molars. Data about dental findings from radiographs is, if at all possible, only comparable with serious limitations. A standardization of both, assessing and reporting entities of dental status from radiographs is missing and has to be established within a report guideline.

Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx

PubMed Central

Weegar, Rebecka; Kvist, Maria; Sundström, Karin; Brunak, Søren; Dalianis, Hercules

2015-01-01

Detection of early symptoms in cervical cancer is crucial for early treatment and survival. To find symptoms of cervical cancer in clinical text, Named Entity Recognition is needed. In this paper the Clinical Entity Finder, a machine-learning tool trained on annotated clinical text from a Swedish internal medicine emergency unit, is evaluated on cervical cancer records. The Clinical Entity Finder identifies entities of the types body part, finding and disorder and is extended with negation detection using the rule-based tool NegEx, to distinguish between negated and non-negated entities. To measure the performance of the tools on this new domain, two physicians annotated a set of clinical notes from the health records of cervical cancer patients. The inter-annotator agreement for finding, disorder and body part obtained an average F-score of 0.677 and the Clinical Entity Finder extended with NegEx had an average F-score of 0.667. PMID:26958270

Finding Cervical Cancer Symptoms in Swedish Clinical Text using a Machine Learning Approach and NegEx.

PubMed

Weegar, Rebecka; Kvist, Maria; Sundström, Karin; Brunak, Søren; Dalianis, Hercules

2015-01-01

Detection of early symptoms in cervical cancer is crucial for early treatment and survival. To find symptoms of cervical cancer in clinical text, Named Entity Recognition is needed. In this paper the Clinical Entity Finder, a machine-learning tool trained on annotated clinical text from a Swedish internal medicine emergency unit, is evaluated on cervical cancer records. The Clinical Entity Finder identifies entities of the types body part, finding and disorder and is extended with negation detection using the rule-based tool NegEx, to distinguish between negated and non-negated entities. To measure the performance of the tools on this new domain, two physicians annotated a set of clinical notes from the health records of cervical cancer patients. The inter-annotator agreement for finding, disorder and body part obtained an average F-score of 0.677 and the Clinical Entity Finder extended with NegEx had an average F-score of 0.667.

Cystic renal tumors: new entities and novel concepts.

PubMed

Moch, Holger

2010-05-01

Cystic renal neoplasms and renal epithelial stromal tumors are diagnostically challenging and represent some novel tumor entities. In this article, clinical and pathologic features of established and novel entities are discussed. Predominantly cystic renal tumors include cystic nephroma/mixed epithelial and stromal tumor, synovial sarcoma, and multilocular cystic renal cell carcinoma. These entities are own tumor entities of the 2004 WHO classification of renal tumors. Tubulocystic carcinoma and acquired cystic disease-associated renal cell carcinoma are neoplasms with an intrinsically cystic growth pattern. Both tumor types should be included in a future WHO classification as novel entities owing to their characteristic features. Cysts and clear cell renal cell carcinoma frequently coexist within the kidneys of patients with von Hippel-Lindau disease. Sporadic clear cell renal cell carcinomas often contain cysts, usually as a minor component. Some clear cell renal cell carcinomas have prominent cysts, and multilocular cystic renal cell carcinoma is composed almost exclusively of cysts. Recent molecular findings suggest that clear cell renal cancer may develop through cyst-dependent and cyst-independent molecular pathways.

CheNER: a tool for the identification of chemical entities and their classes in biomedical literature.

PubMed

Usié, Anabel; Cruz, Joaquim; Comas, Jorge; Solsona, Francesc; Alves, Rui

2015-01-01

Small chemical molecules regulate biological processes at the molecular level. Those molecules are often involved in causing or treating pathological states. Automatically identifying such molecules in biomedical text is difficult due to both, the diverse morphology of chemical names and the alternative types of nomenclature that are simultaneously used to describe them. To address these issues, the last BioCreAtIvE challenge proposed a CHEMDNER task, which is a Named Entity Recognition (NER) challenge that aims at labelling different types of chemical names in biomedical text. To address this challenge we tested various approaches to recognizing chemical entities in biomedical documents. These approaches range from linear Conditional Random Fields (CRFs) to a combination of CRFs with regular expression and dictionary matching, followed by a post-processing step to tag those chemical names in a corpus of Medline abstracts. We named our best performing systems CheNER. We evaluate the performance of the various approaches using the F-score statistics. Higher F-scores indicate better performance. The highest F-score we obtain in identifying unique chemical entities is 72.88%. The highest F-score we obtain in identifying all chemical entities is 73.07%. We also evaluate the F-Score of combining our system with ChemSpot, and find an increase from 72.88% to 73.83%. CheNER presents a valid alternative for automated annotation of chemical entities in biomedical documents. In addition, CheNER may be used to derive new features to train newer methods for tagging chemical entities. CheNER can be downloaded from http://metres.udl.cat and included in text annotation pipelines.

A method of constructing geo-object ontology in disaster system for prevention and decrease

NASA Astrophysics Data System (ADS)

Li, Bin; Liu, Jiping; Shi, Lihong; Wang, Zhenfeng

2009-10-01

A kind of formal system, which can express clearly a certain entity or information, is needed to express geographical concept. Besides, some rules explaining the interrelationship and action between different components are also required. Therefore, the conception of geo-object ontology is introduced. It is a shared formalization and display specification of conceptual knowledge system in the field of concrete application of spatial information science. It can constitute hierarchy structure, which derives from the concept classification system in the geographical area. Its concepts can be described by the property. Property sets can form a vector space with multi-dimensional characteristics. Geographic space is composed of different types of geographic entities. And its concept is formed by a series of geographic entities with the same properties and actions. Moreover, each of the geographic entities can be mapped to an object, and each object has its spatial property, time information and topology, semantic relationships associated with other objects. The biggest difference between ecumenical information ontology and geo-ontology is that the latter has the spatial characteristics. During the construction process of geo-object ontology, some important components, such as geographic type, spatial relation, spatial entity type and coordinates, time, should be included to make further research. Here, taking disaster as an example, by using Protégé and OWL, combined methods used by constructing the geo-object ontology in the form of being manual made by domanial experts and semi-automatic are investigated oriented to disaster to serve ultimately geographic information retrieval service driven by ontology.

45 CFR 2517.400 - What must a State Commission or grantmaking entity include in an application for a grant?

Code of Federal Regulations, 2014 CFR

2014-10-01

... Public Welfare (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE COMMUNITY-BASED SERVICE-LEARNING PROGRAMS Application Contents § 2517.400 What must a State Commission or grantmaking entity... promoting service-learning through programs under this part. The plan must describe the types of community...

45 CFR 2517.400 - What must a State Commission or grantmaking entity include in an application for a grant?

Code of Federal Regulations, 2013 CFR

2013-10-01

... Public Welfare (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE COMMUNITY-BASED SERVICE-LEARNING PROGRAMS Application Contents § 2517.400 What must a State Commission or grantmaking entity... promoting service-learning through programs under this part. The plan must describe the types of community...

45 CFR 2517.400 - What must a State Commission or grantmaking entity include in an application for a grant?

Code of Federal Regulations, 2012 CFR

2012-10-01

... Public Welfare (Continued) CORPORATION FOR NATIONAL AND COMMUNITY SERVICE COMMUNITY-BASED SERVICE-LEARNING PROGRAMS Application Contents § 2517.400 What must a State Commission or grantmaking entity... promoting service-learning through programs under this part. The plan must describe the types of community...

Guidelines for applying the Composite Specification Model (CSM)

NASA Technical Reports Server (NTRS)

Agresti, William

1987-01-01

The Composite Specification Model (CSM) is an approach to representing software requirements. Guidelines are provided for applying CSM and developing each of the three descriptive views of the software: the contextual view, using entities and relationships; the dynamic view, using states and transitions; and the function view, using data flows and processes. Using CSM results in a software specification document, which is outlined.

Viewpoint: Exorcizing Maxwell’s demon

DOE PAGES

Deffner, Sebastian

2015-12-01

Here, physicists have been haunted by the idea of Maxwell's demon for almost 150 years. The beast, conjured in a thought experiment by James Clerk Maxwell, sorts particles in a gas according to their speeds, thus transferring heat from the colder, evenly mixed gas to the region containing the hotter, high-speed particles. At first sight, the demon appears to violate the second law of thermodynamics. But the paradox can be resolved by realizing that work must be performed on the demon for it to do its job properly. This description isn’t entirely satisfying, however, as it introduces an external—not necessarilymore » physical—entity to do work on the demon. Jukka Pekola and colleagues of Aalto University in Finland [1] have now exorcised such nonphysical beings by realizing a nanodevice equivalent to a Maxwell's demon (Fig. 1), but one whose operation doesn’t depend on an external entity. This so-called autonomous device, also known as an information machine, is completely self-contained. So far, autonomous demons have been a purely theoretical concept; this new experimental system provides a way to test formulations of fundamental axioms of thermodynamics and descriptions of information processing.« less

The glia of the adult Drosophila nervous system

PubMed Central

Kremer, Malte C.; Jung, Christophe; Batelli, Sara; Rubin, Gerald M.

2017-01-01

Glia play crucial roles in the development and homeostasis of the nervous system. While the GLIA in the Drosophila embryo have been well characterized, their study in the adult nervous system has been limited. Here, we present a detailed description of the glia in the adult nervous system, based on the analysis of some 500 glial drivers we identified within a collection of synthetic GAL4 lines. We find that glia make up ∼10% of the cells in the nervous system and envelop all compartments of neurons (soma, dendrites, axons) as well as the nervous system as a whole. Our morphological analysis suggests a set of simple rules governing the morphogenesis of glia and their interactions with other cells. All glial subtypes minimize contact with their glial neighbors but maximize their contact with neurons and adapt their macromorphology and micromorphology to the neuronal entities they envelop. Finally, glial cells show no obvious spatial organization or registration with neuronal entities. Our detailed description of all glial subtypes and their regional specializations, together with the powerful genetic toolkit we provide, will facilitate the functional analysis of glia in the mature nervous system. GLIA 2017 GLIA 2017;65:606–638 PMID:28133822

[Can men be included in the population subjected to puerperal psychosis? A case report].

PubMed

Colombel, M; Rebillard, C; Nathou, C; Dollfus, S

2016-08-01

Puerperal psychosis (PP) is a psychiatric disorder that occurs in 1 out of 1000 pregnancies. Well known since antiquity, its symptoms have often been described in mothers, but few studies have successfully investigated a related disorder in fathers. The characteristic of this pathology is more related to its appearance than to its semiological description which is why its nosographic place is always discussed. The objective here is to focus on the definition of PP and to suggest an entity for both genders. Our case report focused on the clinical description of an eighteen-year-old man suffering from an acute psychosis episode that occurred around the birth of his first child. Delusion followed a sudden decline in mood that lasted for a short period of time during the course of the third trimester of his wife's pregnancy. The delirium was rich with auditory and cenesthesic hallucinations, pregnancy and birth denial, feeling movements and hearing voices in his stomach. The symptoms disappeared after one month of treatment via an antipsychotic drug, risperidone. We can confirm that the symptomatic description of the disorder in this patient fits the classical descriptions of PP. Two elements make the PP different from other acute psychoses: the context of pregnancy and delirium focused on the child which can lead to a child murder. The absence of a framework precisely defining the PP does not improve its prevention and can lead to legal attitudes rather than medical care. Men suffering from acute psychosis in a context of pregnancy are submitted to the same risks as women. It is necessary to emphasize descriptions of PP in men to redefine the disease and consider that this entity involves both men and women. Copyright © 2016 L’Encéphale, Paris. Published by Elsevier Masson SAS. All rights reserved.

A New Replicator: A theoretical framework for analysing replication

PubMed Central

2010-01-01

Background Replicators are the crucial entities in evolution. The notion of a replicator, however, is far less exact than the weight of its importance. Without identifying and classifying multiplying entities exactly, their dynamics cannot be determined appropriately. Therefore, it is importance to decide the nature and characteristics of any multiplying entity, in a detailed and formal way. Results Replication is basically an autocatalytic process which enables us to rest on the notions of formal chemistry. This statement has major implications. Simple autocatalytic cycle intermediates are considered as non-informational replicators. A consequence of which is that any autocatalytically multiplying entity is a replicator, be it simple or overly complex (even nests). A stricter definition refers to entities which can inherit acquired changes (informational replicators). Simple autocatalytic molecules (and nests) are excluded from this group. However, in turn, any entity possessing copiable information is to be named a replicator, even multicellular organisms. In order to deal with the situation, an abstract, formal framework is presented, which allows the proper identification of various types of replicators. This sheds light on the old problem of the units and levels of selection and evolution. A hierarchical classification for the partition of the replicator-continuum is provided where specific replicators are nested within more general ones. The classification should be able to be successfully applied to known replicators and also to future candidates. Conclusion This paper redefines the concept of the replicator from a bottom-up theoretical approach. The formal definition and the abstract models presented can distinguish between among all possible replicator types, based on their quantity of variable and heritable information. This allows for the exact identification of various replicator types and their underlying dynamics. The most important claim is that replication, in general, is basically autocatalysis, with a specific defined environment and selective force. A replicator is not valid unless its working environment, and the selective force to which it is subject, is specified. PMID:20219099

On the application of semantic technologies to the domain of forensic investigations in financial crimes

NASA Astrophysics Data System (ADS)

Scheidat, Tobias; Merkel, Ronny; Krummel, Volker; Gerlach, Andreas; Weisensee, Michala; Zeihe, Jana; Dittmann, Jana

2017-10-01

In daily police practice, forensic investigation of criminal cases is mainly based on manual work and the experience of individual forensic experts, using basic storage and data processing technologies. However, an individual criminal case does not only consist of the actual offence, but also of a variety of different aspects involved. For example, in order to solve a financial criminal case, an investigator has to find interrelations between different case entities as well as to other cases. The required information about these different entities is often stored in various databases and mostly requires to be manually requested and processed by forensic investigators. We propose the application of semantic technologies to the domain of forensic investigations at the example of financial crimes. Such combination allows for modelling specific case entities and their interrelations within and between cases. As a result, an explorative search of connections between case entities in the scope of an investigation as well as an automated derivation of conclusions from an established fact base is enabled. The proposed model is presented in the form of a crime field ontology, based on different types of knowledge obtained from three individual sources: open source intelligence, forensic investigators and captive interviews of detained criminals. The modelled crime field ontology is illustrated at two examples using the well known crime type of explosive attack on ATM and the potentially upcoming crime type data theft by NFC crowd skimming. Of these criminal modi operandi, anonymized fictional are modelled, visualized and exploratively searched. Modelled case entities include modi operandi, events, actors, resources, exploited weaknesses as well as flows of money, data and know how. The potential exploration of interrelations between the different case entities of such examples is illustrated in the scope of a fictitious investigation, highlighting the potential of the approach.

Demons syndrome revisited: a review of the literature.

PubMed

Brun, Jean-Luc

2007-06-01

To report various descriptions of the combination of a benign genital tumour with pleural and/or abdominal effusion throughout the years and to determine the paternity of this syndrome, commonly known as Meigs' syndrome. A systematic review of the literature from 1728 to 2004. Before 1880, publications were rare and limited to clinical and anatomical descriptions drawing no conclusions between the cause and effect of this condition and even less about its management. Demons described the syndrome between 1887 and 1902. He was the first to specify that removal of the tumour (benign ovarian cyst, solid ovarian tumour, fibroma of the broad ligament) was essential for the patient to be cured of the effusions and that it was wrong to postpone surgery. In 1937, Meigs arrived at the same findings concerning ovarian fibromas and granulosa cell tumours, hence the name of Demons-Meigs which was given to this syndrome with the agreement of Meigs. Current literature reports on pseudosyndromes of Demons-Meigs including genital malignancies with negative cytology. These entities should not be called Demons or Meigs pseudosyndromes. Inversely, all benign tumours of the genital tract should be included in Demons syndrome, even if Demons did not actually encounter any during his years of practice, but it was in the spirit of his observations. Demons' syndrome includes all benign genital tumours, the Demons-Meigs eponym is reserved for the description of ovarian fibromas and granulosa cell tumours, and the Demons' pseudosyndrome includes all other entities.

New tumor entities in the 4th edition of the World Health Organization classification of head and neck tumors: Nasal cavity, paranasal sinuses and skull base.

PubMed

Thompson, Lester D R; Franchi, Alessandro

2018-03-01

The World Health Organization recently published the 4th edition of the Classification of Head and Neck Tumors, including several new entities, emerging entities, and significant updates to the classification and characterization of tumor and tumor-like lesions, specifically as it relates to nasal cavity, paranasal sinuses, and skull base in this overview. Of note, three new entities (NUT carcinoma, seromucinous hamartoma, biphenotypic sinonasal sarcoma,) were added to this section, while emerging entities (SMARCB1-deficient carcinoma and HPV-related carcinoma with adenoid cystic-like features) and several tumor-like entities (respiratory epithelial adenomatoid hamartoma, chondromesenchymal hamartoma) were included as provisional diagnoses or discussed in the setting of the differential diagnosis. The sinonasal tract houses a significant diversity of entities, but interestingly, the total number of entities has been significantly reduced by excluding tumor types if they did not occur exclusively or predominantly at this site or if they are discussed in detail elsewhere in the book. Refinements to nomenclature and criteria were provided to sinonasal papilloma, borderline soft tissue tumors, and neuroendocrine neoplasms. Overall, the new WHO classification reflects the state of current understanding for many relatively rare neoplasms, with this article highlighting the most significant changes.

Semantic modeling of the structural and process entities during plastic deformation of crystals and rocks

NASA Astrophysics Data System (ADS)

Babaie, Hassan; Davarpanah, Armita

2016-04-01

We are semantically modeling the structural and dynamic process components of the plastic deformation of minerals and rocks in the Plastic Deformation Ontology (PDO). Applying the Ontology of Physics in Biology, the PDO classifies the spatial entities that participate in the diverse processes of plastic deformation into the Physical_Plastic_Deformation_Entity and Nonphysical_Plastic_Deformation_Entity classes. The Material_Physical_Plastic_Deformation_Entity class includes things such as microstructures, lattice defects, atoms, liquid, and grain boundaries, and the Immaterial_Physical_Plastic_Deformation_Entity class includes vacancies in crystals and voids along mineral grain boundaries. The objects under the many subclasses of these classes (e.g., crystal, lattice defect, layering) have spatial parts that are related to each other through taxonomic (e.g., Line_Defect isA Lattice_Defect), structural (mereological, e.g., Twin_Plane partOf Twin), spatial-topological (e.g., Vacancy adjacentTo Atom, Fluid locatedAlong Grain_Boundary), and domain specific (e.g., displaces, Fluid crystallizes Dissolved_Ion, Void existsAlong Grain_Boundary) relationships. The dynamic aspect of the plastic deformation is modeled under the dynamical Process_Entity class that subsumes classes such as Recrystallization and Pressure_Solution that define the flow of energy amongst the physical entities. The values of the dynamical state properties of the physical entities (e.g., Chemical_Potential, Temperature, Particle_Velocity) change while they take part in the deformational processes such as Diffusion and Dislocation_Glide. The process entities have temporal parts (phases) that are related to each other through temporal relations such as precedes, isSubprocessOf, and overlaps. The properties of the physical entities, defined under the Physical_Property class, change as they participate in the plastic deformational processes. The properties are categorized into dynamical, constitutive, spatial, temporal, statistical, and thermodynamical. The dynamical properties, categorized under the Dynamical_Rate_Property and Dynamical_State_Property classes, subsume different classes of properties (e.g., Fluid_Flow_Rate, Temperature, Chemical_Potential, Displacement, Electrical_Charge) based on the physical domain (e.g., fluid, heat, chemical, solid, electrical). The properties are related to the objects under the Physical_Entity class through diverse object type (e.g., physicalPropertyOf) and data type (e.g., Fluid_Pressure unit 'MPa') properties. The changes of the dynamical properties of the physical entities, described by the empirical laws (equations) modeled by experimental structural geologists, are modeled through the Physical_Property_Dependency class that subsumes the more specialized constitutive, kinetic, and thermodynamic expressions of the relationships among the dynamic properties. Annotation based on the PDO will make it possible to integrate and reuse experimental plastic deformation data, knowledge, and simulation models, and conduct semantic-based search of the source data originating from different rock testing laboratories.

The psychology of corporate rights: Perception of corporate versus individual rights to religious liberty, privacy, and free speech.

PubMed

Mentovich, Avital; Huq, Aziz; Cerf, Moran

2016-04-01

The U.S. Supreme Court has increasingly expanded the scope of constitutional rights granted to corporations and other collective entities. Although this tendency receives widespread public and media attention, little empirical research examines how people ascribe rights, commonly thought to belong to natural persons, to corporations. This article explores this issue in 3 studies focusing on different rights (religious liberty, privacy, and free speech). We examined participants' willingness to grant a given right while manipulating the type of entity at stake (from small businesses, to larger corporations, to for-profit and nonprofit companies), and the identity of the right holder (from employees, to owners, to the company itself as a separate entity). We further examined the role of political ideology in perceptions of rights. Results indicated a significant decline in the degree of recognition of entities' rights (the company itself) in comparison to natural persons' rights (owners and employees). Results also demonstrated an effect of the type of entity at stake: Larger, for-profit businesses were less likely to be viewed as rights holders compared with nonprofit entities. Although both tendencies persisted across the ideological spectrum, ideological differences emerged in the relations between corporate and individual rights: these were positively related among conservatives but negatively related among liberals. Finally, we found that the desire to protect citizens (compared with businesses) underlies individuals' willingness to grant rights to companies. These findings show that people (rather than corporations) are more appropriate recipients of rights, and can explain public backlash to judicial expansions of corporate rights. (c) 2016 APA, all rights reserved).

Burning mouth syndrome.

PubMed

Jääskeläinen, Satu K; Woda, Alain

2017-06-01

Objective To review the clinical entity of primary burning mouth syndrome (BMS), its pathophysiological mechanisms, accurate new diagnostic methods and evidence-based treatment options, and to describe novel lines for future research regarding aetiology, pathophysiology, and new therapeutic strategies. Description Primary BMS is a chronic neuropathic intraoral pain condition that despite typical symptoms lacks clear clinical signs of neuropathic involvement. With advanced diagnostic methods, such as quantitative sensory testing of small somatosensory and taste afferents, neurophysiological recordings of the trigeminal system, and peripheral nerve blocks, most BMS patients can be classified into the peripheral or central type of neuropathic pain. These two types differ regarding pathophysiological mechanisms, efficacy of available treatments, and psychiatric comorbidity. The two types may overlap in individual patients. BMS is most frequent in postmenopausal women, with general population prevalence of around 1%. Treatment of BMS is difficult; best evidence exists for efficacy of topical and systemic clonazepam. Hormonal substitution, dopaminergic medications, and therapeutic non-invasive neuromodulation may provide efficient mechanism-based treatments for BMS in the future. Conclusion We present a novel comprehensive hypothesis of primary BMS, gathering the hormonal, neuropathic, and genetic factors presumably required in the genesis of the condition. This will aid in future research on pathophysiology and risk factors of BMS, and boost treatment trials taking into account individual mechanism profiles and subgroup-clusters.

The Development of Children's Ability to Use Evidence to Infer Reality Status

ERIC Educational Resources Information Center

Tullos, Ansley; Woolley, Jacqueline D.

2009-01-01

These studies investigate children's use of scientific reasoning to infer the reality status of novel entities. Four- to 8-year-olds heard about novel entities and were asked to infer their reality status from 3 types of evidence: supporting evidence, irrelevant evidence, and no evidence. Experiment 1 revealed that children used supporting versus…

Pediatric Type Follicular Lymphoma: A Rare Entity with Excellent Prognosis

DTIC Science & Technology

2018-01-19

lymphomas, has a median age range of 7.5-11.7, and has a male- female ratio of 4:1. This entity occurs most frequently in the tonsils and head and... neck lymph nodes. The pathogenesis of follicular lymphoma in adults is based upon immunoglobulin gene rearrangements with BCL2, BCL6, and MYC

A Cross-disciplinary Framework for the Description of Contextually Mediated Change

NASA Astrophysics Data System (ADS)

Gabora, Liane; Aerts, Diederik

We present a mathematical framework (referred to as Context-driven Actualization of Potential, or CAP) for describing how entities change over time under the influence of a context. The approach facilitates comparison of change of state of entities studied in different disciplines. Processes are seen to differ according to the degree of nondeterminism, and the degree to which they are sensitive to, internalize, and depend upon a particular context. Our analysis suggests that the dynamical evolution of a quantum entity described by the Schrödinger equation is not fundamentally different from change provoked by a measurement often referred to as collapse but a limiting case, with only one way to collapse. The biological transition to coded replication is seen as a means of preserving structure in the face of context, and sexual replication as a means of increasing potentiality thus enhancing diversity through interaction with context. The framework sheds light on concepts like selection and fitness, reveals how exceptional Darwinian evolution is as a means of 'change of state', and clarifies in what sense culture (and the creative process underlying it) are Darwinian.

["Scrap" as an element of communication in nursing].

PubMed

Esperidião, E; Medeiros Teixeira, M E; Rodrigues Stacciarini, J M

1996-04-01

Based on the understanding that students and nursing professionals demonstrate difficulties in being a "person" in the profession, we developed a descriptive and exploratory study with a qualitative approach. Then, we offered during the "Iind" II Nursing Congress in the city of Goiania a work-shop called "LEARNING ABOUT NURSE'S ENTITY". Among various processes of work-groups; the "Scrap" was used as a kind of communication. It was a resource utilized in certain dynamics, being the object of our study that has the following goals: to identify the representation of nurse's "entity", to verify the interaction process "man-scrap" during the realization of the work and to verify if the object is represented as it really is. We have seen that there are particularities in the representation of nurse's entity. Regarding "man-scrap" interaction it had the followed sequence: finding strange the material and the proposal of work, manipulating and identifying objects, "scrap" selection and concretion of the job. With respect to the objects, we perceived a clear preference to the ones related to the profession. Finally, we suggest that other studies about the "scrap" communication element, must be developed.

SPECTRa-T: machine-based data extraction and semantic searching of chemistry e-theses.

PubMed

Downing, Jim; Harvey, Matt J; Morgan, Peter B; Murray-Rust, Peter; Rzepa, Henry S; Stewart, Diana C; Tonge, Alan P; Townsend, Joe A

2010-02-22

The SPECTRa-T project has developed text-mining tools to extract named chemical entities (NCEs), such as chemical names and terms, and chemical objects (COs), e.g., experimental spectral assignments and physical chemistry properties, from electronic theses (e-theses). Although NCEs were readily identified within the two major document formats studied, only the use of structured documents enabled identification of chemical objects and their association with the relevant chemical entity (e.g., systematic chemical name). A corpus of theses was analyzed and it is shown that a high degree of semantic information can be extracted from structured documents. This integrated information has been deposited in a persistent Resource Description Framework (RDF) triple-store that allows users to conduct semantic searches. The strength and weaknesses of several document formats are reviewed.

76 FR 38187 - International Conference on Harmonisation; Draft Guidance on Q11 Development and Manufacture of...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-29

...The Food and Drug Administration (FDA) is announcing the availability of a draft guidance entitled ``Q11 Development and Manufacture of Drug Substances.'' The draft guidance was prepared under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). The draft guidance describes approaches to developing process and drug substance understanding and provides guidance on what information should be provided in certain sections of the Common Technical Document (CTD). The draft guidance is intended to harmonize the scientific and technical principles relating to the description and justification of the development and manufacturing process of drug substances (both chemical entities and biotechnological/biological entities) to enable a consistent approach for providing and evaluating this information across the three regions.

[Botulinum toxin type A in headache treatment : Established and experimental indications].

PubMed

Gaul, C; Holle-Lee, D; Straube, A

2016-08-01

In recent years botulinum toxin type A has been used increasingly more in the treatment of specific headache disorders. Especially regarding chronic migraine with and without combined medication overuse, convincing randomized studies have proven the efficacy of this treatment option and have led to approval for this indication. Regarding other headache entities, such as episodic migraine, tension-type headache, trigeminal autonomic cephalalgia (TAC), neuralgic, neuropathic and myofascial pain, currently available scientific data on the efficacy of botulinum toxin type A are scarce and often ambiguous. The exact underlying mechanisms of the influence of botulinum toxin type A on the pathophysiology of headache are not completely clear but an influence on the release of calcitonin gene-related peptide (CGRP) seems to play a crucial role. This article summarizes the most important studies as well as experiences of treatment with botulinum toxin type A regarding different headache entities.

Phacomatosis pigmentokeratotica: another epidermal nevus syndrome and a distinctive type of twin spotting.

PubMed

Boente, M C; Pizzi de Parra, N; Larralde de Luna, M; Bonet, H B; Santos Muñoz, A; Parra, V; Gramajo, P; Moreno, S; Asial, R A

2000-01-01

The name epidermal nevus syndrome could be applied to a group of clinically and histopathologically different entities as has been pointed out by Happle. Phacomatosis pigmentokeratotica is a further type of epidermal nevus syndrome distinguished by the presence of a sebaceous nevus and a contralateral speckled lentiginous nevus of the papular type, associated with skeletal or neurological abnormalities. Three new cases of this recently delineated syndrome are presented. A common origin may account for the temporal and spatial relationship between the epidermal and the speckled lentiginous nevus. The concept of melanocytic-epidermal twin spotting similar to the interpretation of vascular twin spotting could explain the pathogenesis of this entity.

Epidemic spreading through direct and indirect interactions.

PubMed

Ganguly, Niloy; Krueger, Tyll; Mukherjee, Animesh; Saha, Sudipta

2014-09-01

In this paper we study the susceptible-infected-susceptible epidemic dynamics, considering a specialized setting where popular places (termed passive entities) are visited by agents (termed active entities). We consider two types of spreading dynamics: direct spreading, where the active entities infect each other while visiting the passive entities, and indirect spreading, where the passive entities act as carriers and the infection is spread via them. We investigate in particular the effect of selection strategy, i.e., the way passive entities are chosen, in the spread of epidemics. We introduce a mathematical framework to study the effect of an arbitrary selection strategy and derive formulas for prevalence, extinction probabilities, and epidemic thresholds for both indirect and direct spreading. We also obtain a very simple relationship between the extinction probability and the prevalence. We pay special attention to preferential selection and derive exact formulas. The analysis reveals that an increase in the diversity in the selection process lowers the epidemic thresholds. Comparing the direct and indirect spreading, we identify regions in the parameter space where the prevalence of the indirect spreading is higher than the direct one.

Epidemic spreading through direct and indirect interactions

NASA Astrophysics Data System (ADS)

Ganguly, Niloy; Krueger, Tyll; Mukherjee, Animesh; Saha, Sudipta

2014-09-01

In this paper we study the susceptible-infected-susceptible epidemic dynamics, considering a specialized setting where popular places (termed passive entities) are visited by agents (termed active entities). We consider two types of spreading dynamics: direct spreading, where the active entities infect each other while visiting the passive entities, and indirect spreading, where the passive entities act as carriers and the infection is spread via them. We investigate in particular the effect of selection strategy, i.e., the way passive entities are chosen, in the spread of epidemics. We introduce a mathematical framework to study the effect of an arbitrary selection strategy and derive formulas for prevalence, extinction probabilities, and epidemic thresholds for both indirect and direct spreading. We also obtain a very simple relationship between the extinction probability and the prevalence. We pay special attention to preferential selection and derive exact formulas. The analysis reveals that an increase in the diversity in the selection process lowers the epidemic thresholds. Comparing the direct and indirect spreading, we identify regions in the parameter space where the prevalence of the indirect spreading is higher than the direct one.

Entity recognition in the biomedical domain using a hybrid approach.

PubMed

Basaldella, Marco; Furrer, Lenz; Tasso, Carlo; Rinaldi, Fabio

2017-11-09

This article describes a high-recall, high-precision approach for the extraction of biomedical entities from scientific articles. The approach uses a two-stage pipeline, combining a dictionary-based entity recognizer with a machine-learning classifier. First, the OGER entity recognizer, which has a bias towards high recall, annotates the terms that appear in selected domain ontologies. Subsequently, the Distiller framework uses this information as a feature for a machine learning algorithm to select the relevant entities only. For this step, we compare two different supervised machine-learning algorithms: Conditional Random Fields and Neural Networks. In an in-domain evaluation using the CRAFT corpus, we test the performance of the combined systems when recognizing chemicals, cell types, cellular components, biological processes, molecular functions, organisms, proteins, and biological sequences. Our best system combines dictionary-based candidate generation with Neural-Network-based filtering. It achieves an overall precision of 86% at a recall of 60% on the named entity recognition task, and a precision of 51% at a recall of 49% on the concept recognition task. These results are to our knowledge the best reported so far in this particular task.

A critical approach to the definition of Darwinian units of selection.

PubMed

Rinkevich, B

2000-12-01

What are the biological units of selection? In fact, the notion of "unit of selection" (UOS) is blurred by ambiguity and controversy. To further evaluate the biological entities that are the objects of natural selection, three novel conceptual criteria (holism, minimalism, functionalism) are critically applied; they reveal, in addition to the self-evident case of the "individual," at least six distinct types of UOSs. These UOSs do not always have a defined structural organization; they can be parts of a living organism, a cohesive group of conspecifics, a multiunit entity, a totipotent cell, a DNA fragment, or a whole organism. UOS types diversify by amalgamation or parcelation processes of apparent entities. Therefore, previous attempts to characterize the UOSs solely on some morphological levels (gene, individual, group) without applying stringent criteria have failed to cope with the structural variations of natural phenomena and have led to the ambiguity of terms used.

Fair market value: taking a proactive approach.

PubMed

Romero, Richard A

2008-04-01

A valuation report assessing the fair market value of a contractual arrangement should include: A description of the company, entity, or circumstance being valued. Analysis of general economic conditions that are expected to affect the enterprise. Evaluation of economic conditions in the medical services industry. Explanation of the various valuation approaches that were considered. Documentation of key underlying assumptions, including revenue and expense projections, projected profit, and ROI.

Strategic Performance Management: Organizing People and Their Work in the SEA of the Future

ERIC Educational Resources Information Center

Redding, Sam; Layland, Allison

2015-01-01

A State Education Agency (SEA), whether in a large state or small, is responsible for a complex education system, responsive to a host of stakeholders, and charged with advocating for a multitude of students of all ages attending schools of every description. Much of what an SEA is tasked with accomplishing is set by external entities, from the…

Cross domains Arabic named entity recognition system

NASA Astrophysics Data System (ADS)

Al-Ahmari, S. Saad; Abdullatif Al-Johar, B.

2016-07-01

Named Entity Recognition (NER) plays an important role in many Natural Language Processing (NLP) applications such as; Information Extraction (IE), Question Answering (QA), Text Clustering, Text Summarization and Word Sense Disambiguation. This paper presents the development and implementation of domain independent system to recognize three types of Arabic named entities. The system works based on a set of domain independent grammar-rules along with Arabic part of speech tagger in addition to gazetteers and lists of trigger words. The experimental results shown, that the system performed as good as other systems with better results in some cases of cross-domains corpora.

Early- and late-onset Alzheimer disease: Are they the same entity?

PubMed

Tellechea, P; Pujol, N; Esteve-Belloch, P; Echeveste, B; García-Eulate, M R; Arbizu, J; Riverol, M

2018-05-01

Early-onset Alzheimer disease (EOAD), which presents in patients younger than 65 years, has frequently been described as having different features from those of late-onset Alzheimer disease (LOAD). This review analyses the most recent studies comparing the clinical presentation and neuropsychological, neuropathological, genetic, and neuroimaging findings of both types in order to determine whether EOAD and LOAD are different entities or distinct forms of the same entity. We observed consistent differences between clinical findings in EOAD and in LOAD. Fundamentally, the onset of EOAD is more likely to be marked by atypical symptoms, and cognitive assessments point to poorer executive and visuospatial functioning and praxis with less marked memory impairment. Alzheimer-type features will be more dense and widespread in neuropathology studies, with structural and functional neuroimaging showing greater and more diffuse atrophy extending to neocortical areas (especially the precuneus). In conclusion, available evidence suggests that EOAD and LOAD are 2 different forms of a single entity. LOAD is likely to be influenced by ageing-related processes. Copyright © 2015 Sociedad Española de Neurología. Publicado por Elsevier España, S.L.U. All rights reserved.

Considering context: reliable entity networks through contextual relationship extraction

NASA Astrophysics Data System (ADS)

David, Peter; Hawes, Timothy; Hansen, Nichole; Nolan, James J.

2016-05-01

Existing information extraction techniques can only partially address the problem of exploiting unreadable-large amounts text. When discussion of events and relationships is limited to simple, past-tense, factual descriptions of events, current NLP-based systems can identify events and relationships and extract a limited amount of additional information. But the simple subset of available information that existing tools can extract from text is only useful to a small set of users and problems. Automated systems need to find and separate information based on what is threatened or planned to occur, has occurred in the past, or could potentially occur. We address the problem of advanced event and relationship extraction with our event and relationship attribute recognition system, which labels generic, planned, recurring, and potential events. The approach is based on a combination of new machine learning methods, novel linguistic features, and crowd-sourced labeling. The attribute labeler closes the gap between structured event and relationship models and the complicated and nuanced language that people use to describe them. Our operational-quality event and relationship attribute labeler enables Warfighters and analysts to more thoroughly exploit information in unstructured text. This is made possible through 1) More precise event and relationship interpretation, 2) More detailed information about extracted events and relationships, and 3) More reliable and informative entity networks that acknowledge the different attributes of entity-entity relationships.

Long-term outcomes of destructive seronegative (rheumatoid) arthritis - description of four clinical cases.

PubMed

Nikiphorou, Elena; Sjöwall, Christopher; Hannonen, Pekka; Rannio, Tuomas; Sokka, Tuulikki

2016-06-03

Seronegative rheumatoid arthritis is associated with a milder course of progression compared to seropositive disease. However, long-term follow-up data of the clinical course of seronegative rheumatoid arthritis are sparse. Here we describe four cases with a rare disease entity of aggressive destructive seronegative (rheumatoid) arthritis with 20-35 years of follow-up. The four cases are women with an initial presentation of seronegative rheumatoid arthritis in 1980-1996 and have received disease-modifying anti-rheumatic drugs since the diagnosis. In all cases, the condition has been refractory to treatments and evolved into a severe disease with destructions of the wrists, sub-talar and ankle joints, as well as large joints but not small joints of fingers and toes. All cases are negative with regard to rheumatoid factor, anti-cyclic citrullinated peptide antibodies and antibodies against carbamylated proteins. This report adds to the existing literature, making the reader aware of this sub-type of inflammatory arthritis which despite being seronegative, can have devastating disease consequences. The report highlights the need for further research into this field in order to better understand this disease sub-type, the pathogenesis, disease course and outcomes.

Imaging Biomarkers for Adult Medulloblastomas: Genetic Entities May Be Identified by Their MR Imaging Radiophenotype.

PubMed

Keil, V C; Warmuth-Metz, M; Reh, C; Enkirch, S J; Reinert, C; Beier, D; Jones, D T W; Pietsch, T; Schild, H H; Hattingen, E; Hau, P

2017-10-01

The occurrence of medulloblastomas in adults is rare; nevertheless, these tumors can be subdivided into genetic and histologic entities each having distinct prognoses. This study aimed to identify MR imaging biomarkers to classify these entities and to uncover differences in MR imaging biomarkers identified in pediatric medulloblastomas. Eligible preoperative MRIs from 28 patients (11 women; 22-53 years of age) of the Multicenter Pilot-study for the Therapy of Medulloblastoma of Adults (NOA-7) cohort were assessed by 3 experienced neuroradiologists. Lesions and perifocal edema were volumetrized and multiparametrically evaluated for classic morphologic characteristics, location, hydrocephalus, and Chang criteria. To identify MR imaging biomarkers, we correlated genetic entities sonic hedgehog ( SHH ) TP53 wild type, wingless ( WNT ), and non -WNT/ non -SHH medulloblastomas (in adults, Group 4), and histologic entities were correlated with the imaging criteria. These MR imaging biomarkers were compared with corresponding data from a pediatric study. There were 19 SHH TP53 wild type (69%), 4 WNT -activated (14%), and 5 Group 4 (17%) medulloblastomas. Six potential MR imaging biomarkers were identified, 3 of which, hydrocephalus ( P = .03), intraventricular macrometastases ( P = .02), and hemorrhage ( P = .04), when combined, could identify WNT medulloblastoma with 100% sensitivity and 88.3% specificity (95% CI, 39.8%-100.0% and 62.6%-95.3%). WNT -activated nuclear β-catenin accumulating medulloblastomas were smaller than the other entities (95% CI, 5.2-22.3 cm 3 versus 35.1-47.6 cm 3 ; P = .03). Hemorrhage was exclusively present in non -WNT/ non -SHH medulloblastomas ( P = .04; n = 2/5). MR imaging biomarkers were all discordant from those identified in the pediatric cohort. Desmoplastic/nodular medulloblastomas were more rarely in contact with the fourth ventricle (4/15 versus 7/13; P = .04). MR imaging biomarkers can help distinguish histologic and genetic medulloblastoma entities in adults and appear to be different from those identified in children. © 2017 by American Journal of Neuroradiology.

Chemical named entities recognition: a review on approaches and applications

PubMed Central

2014-01-01

The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is very rich with information about chemical entities. Extracting molecules and their related properties and activities from the scientific literature to “text mine” these extracted data and determine contextual relationships helps research scientists, particularly those in drug development. One of the most important challenges in chemical text mining is the recognition of chemical entities mentioned in the texts. In this review, the authors briefly introduce the fundamental concepts of chemical literature mining, the textual contents of chemical documents, and the methods of naming chemicals in documents. We sketch out dictionary-based, rule-based and machine learning, as well as hybrid chemical named entity recognition approaches with their applied solutions. We end with an outlook on the pros and cons of these approaches and the types of chemical entities extracted. PMID:24834132

Chemical named entities recognition: a review on approaches and applications.

PubMed

Eltyeb, Safaa; Salim, Naomie

2014-01-01

The rapid increase in the flow rate of published digital information in all disciplines has resulted in a pressing need for techniques that can simplify the use of this information. The chemistry literature is very rich with information about chemical entities. Extracting molecules and their related properties and activities from the scientific literature to "text mine" these extracted data and determine contextual relationships helps research scientists, particularly those in drug development. One of the most important challenges in chemical text mining is the recognition of chemical entities mentioned in the texts. In this review, the authors briefly introduce the fundamental concepts of chemical literature mining, the textual contents of chemical documents, and the methods of naming chemicals in documents. We sketch out dictionary-based, rule-based and machine learning, as well as hybrid chemical named entity recognition approaches with their applied solutions. We end with an outlook on the pros and cons of these approaches and the types of chemical entities extracted.

Hybrid approaches for multiple-species stochastic reaction-diffusion models

NASA Astrophysics Data System (ADS)

Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

2015-10-01

Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

Hybrid approaches for multiple-species stochastic reaction-diffusion models.

PubMed

Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K; Byrne, Helen

2015-10-15

Reaction-diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction-diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model.

Hybrid approaches for multiple-species stochastic reaction–diffusion models

PubMed Central

Spill, Fabian; Guerrero, Pilar; Alarcon, Tomas; Maini, Philip K.; Byrne, Helen

2015-01-01

Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and small in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. PMID:26478601

LeadMine: a grammar and dictionary driven approach to entity recognition.

PubMed

Lowe, Daniel M; Sayle, Roger A

2015-01-01

Chemical entity recognition has traditionally been performed by machine learning approaches. Here we describe an approach using grammars and dictionaries. This approach has the advantage that the entities found can be directly related to a given grammar or dictionary, which allows the type of an entity to be known and, if an entity is misannotated, indicates which resource should be corrected. As recognition is driven by what is expected, if spelling errors occur, they can be corrected. Correcting such errors is highly useful when attempting to lookup an entity in a database or, in the case of chemical names, converting them to structures. Our system uses a mixture of expertly curated grammars and dictionaries, as well as dictionaries automatically derived from public resources. We show that the heuristics developed to filter our dictionary of trivial chemical names (from PubChem) yields a better performing dictionary than the previously published Jochem dictionary. Our final system performs post-processing steps to modify the boundaries of entities and to detect abbreviations. These steps are shown to significantly improve performance (2.6% and 4.0% F1-score respectively). Our complete system, with incremental post-BioCreative workshop improvements, achieves 89.9% precision and 85.4% recall (87.6% F1-score) on the CHEMDNER test set. Grammar and dictionary approaches can produce results at least as good as the current state of the art in machine learning approaches. While machine learning approaches are commonly thought of as "black box" systems, our approach directly links the output entities to the input dictionaries and grammars. Our approach also allows correction of errors in detected entities, which can assist with entity resolution.

Mesh Oriented datABase

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

Tautges, Timothy J.

MOAB is a component for representing and evaluating mesh data. MOAB can store stuctured and unstructured mesh, consisting of elements in the finite element "zoo". The functional interface to MOAB is simple yet powerful, allowing the representation of many types of metadata commonly found on the mesh. MOAB is optimized for efficiency in space and time, based on access to mesh in chunks rather than through individual entities, while also versatile enough to support individual entity access. The MOAB data model consists of a mesh interface instance, mesh entities (vertices and elements), sets, and tags. Entities are addressed through handlesmore » rather than pointers, to allow the underlying representation of an entity to change without changing the handle to that entity. Sets are arbitrary groupings of mesh entities and other sets. Sets also support parent/child relationships as a relation distinct from sets containing other sets. The directed-graph provided by set parent/child relationships is useful for modeling topological relations from a geometric model or other metadata. Tags are named data which can be assigned to the mesh as a whole, individual entities, or sets. Tags are a mechanism for attaching data to individual entities and sets are a mechanism for describing relations between entities; the combination of these two mechanisms isa powerful yet simple interface for representing metadata or application-specific data. For example, sets and tags can be used together to describe geometric topology, boundary condition, and inter-processor interface groupings in a mesh. MOAB is used in several ways in various applications. MOAB serves as the underlying mesh data representation in the VERDE mesh verification code. MOAB can also be used as a mesh input mechanism, using mesh readers induded with MOAB, or as a t’anslator between mesh formats, using readers and writers included with MOAB.« less

LeadMine: a grammar and dictionary driven approach to entity recognition

PubMed Central

2015-01-01

Background Chemical entity recognition has traditionally been performed by machine learning approaches. Here we describe an approach using grammars and dictionaries. This approach has the advantage that the entities found can be directly related to a given grammar or dictionary, which allows the type of an entity to be known and, if an entity is misannotated, indicates which resource should be corrected. As recognition is driven by what is expected, if spelling errors occur, they can be corrected. Correcting such errors is highly useful when attempting to lookup an entity in a database or, in the case of chemical names, converting them to structures. Results Our system uses a mixture of expertly curated grammars and dictionaries, as well as dictionaries automatically derived from public resources. We show that the heuristics developed to filter our dictionary of trivial chemical names (from PubChem) yields a better performing dictionary than the previously published Jochem dictionary. Our final system performs post-processing steps to modify the boundaries of entities and to detect abbreviations. These steps are shown to significantly improve performance (2.6% and 4.0% F1-score respectively). Our complete system, with incremental post-BioCreative workshop improvements, achieves 89.9% precision and 85.4% recall (87.6% F1-score) on the CHEMDNER test set. Conclusions Grammar and dictionary approaches can produce results at least as good as the current state of the art in machine learning approaches. While machine learning approaches are commonly thought of as "black box" systems, our approach directly links the output entities to the input dictionaries and grammars. Our approach also allows correction of errors in detected entities, which can assist with entity resolution. PMID:25810776

Whole Trait Theory

PubMed Central

Fleeson, William; Jayawickreme, Eranda

2014-01-01

Personality researchers should modify models of traits to include mechanisms of differential reaction to situations. Whole Trait Theory does so via five main points. First, the descriptive side of traits should be conceptualized as density distributions of states. Second, it is important to provide an explanatory account of the Big 5 traits. Third, adding an explanatory account to the Big 5 creates two parts to traits, an explanatory part and a descriptive part, and these two parts should be recognized as separate entities that are joined into whole traits. Fourth, Whole Trait Theory proposes that the explanatory side of traits consists of social-cognitive mechanisms. Fifth, social-cognitive mechanisms that produce Big-5 states should be identified. PMID:26097268

[Role of the sympathetic nervous system in vasovagal syncope and rationale for beta-blockers and norepinephrine transporter inhibitors].

PubMed

Márquez, Manlio F; Gómez-Flores, Jorge Rafael; González-Hermosillo, Jesús A; Ruíz-Siller, Teresita de Jesús; Cárdenas, Manuel

2016-12-29

Vasovagal or neurocardiogenic syncope is a common clinical situation and, as with other entities associated with orthostatic intolerance, the underlying condition is a dysfunction of the autonomic nervous system. This article reviews various aspects of vasovagal syncope, including its relationship with orthostatic intolerance and the role of the autonomic nervous system in it. A brief history of the problem is given, as well as a description of how the names and associated concepts have evolved. The response of the sympathetic system to orthostatic stress, the physiology of the baroreflex system and the neurohumoral changes that occur with standing are analyzed. Evidence is presented of the involvement of the autonomic nervous system, including studies of heart rate variability, microneurography, cardiac innervation, and molecular genetic studies. Finally, we describe different studies on the use of beta-blockers and norepinephrine transporter inhibitors (sibutramine, reboxetine) and the rationality of their use to prevent this type of syncope. Creative Commons

EcoCyc: a comprehensive database resource for Escherichia coli

PubMed Central

Keseler, Ingrid M.; Collado-Vides, Julio; Gama-Castro, Socorro; Ingraham, John; Paley, Suzanne; Paulsen, Ian T.; Peralta-Gil, Martín; Karp, Peter D.

2005-01-01

The EcoCyc database (http://EcoCyc.org/) is a comprehensive source of information on the biology of the prototypical model organism Escherichia coli K12. The mission for EcoCyc is to contain both computable descriptions of, and detailed comments describing, all genes, proteins, pathways and molecular interactions in E.coli. Through ongoing manual curation, extensive information such as summary comments, regulatory information, literature citations and evidence types has been extracted from 8862 publications and added to Version 8.5 of the EcoCyc database. The EcoCyc database can be accessed through a World Wide Web interface, while the downloadable Pathway Tools software and data files enable computational exploration of the data and provide enhanced querying capabilities that web interfaces cannot support. For example, EcoCyc contains carefully curated information that can be used as training sets for bioinformatics prediction of entities such as promoters, operons, genetic networks, transcription factor binding sites, metabolic pathways, functionally related genes, protein complexes and protein–ligand interactions. PMID:15608210

An Analysis of the Modes and States for Generic Avionics

NASA Technical Reports Server (NTRS)

Wray, Richard B.

1993-01-01

The objective of this study was to develop a topology for describing the behavior of mission, vehicle and system/substem entities in new flight vehicle designs based on the use of open standards. It also had to define and describe the modes and states which may be used in generic avionics behavioral descriptions, describe their interrelationships, and establish a method for applying generic avionics to actual flight vehicle designs.

[Rudimentary horn pregnancy diagnostic: difficulties and therapeutic management].

PubMed

Mamouni, Nisrine; Ghazal, Nabil; Erraghay, Sanaa; Bouchikhi, Chahrazed; Banani, Abdelaziz

2016-01-01

The occurrence of rudimentary horn pregnancy is an extremely rare and potentially serious obstetric entity, threatening maternal and fetal outcome. The authors report five cases of rudimentary horn pregnancy, the difficulties in making a proper diagnosis and the therapeutic management of this pathological entity, stressing the importance of transvaginal ultrasound, of pelvic MRI and laparoscopy in the early diagnosis of this type of uterine malformation.

Between Oais and Agile a Dynamic Data Management Approach

NASA Astrophysics Data System (ADS)

Bennett, V. L.; Conway, E. A.; Waterfall, A. M.; Pepler, S.

2015-12-01

In this paper we decribe an approach to the integration of existing archival activities which lies between compliance with the more rigid OAIS/TRAC standards and a more flexible "Agile" approach to the curation and preservation of Earth Observation data. We provide a high level overview of existing practice and discuss how these procedures can be extended and supported through the description of preservation state. The aim of which is to facilitate the dynamic controlled management of scientific data through its lifecycle. While processes are considered they are not statically defined but rather driven by human interactions in the form of risk management/review procedure that produce actionable plans, which are responsive to change. We then proceed by describing the feasibility testing of extended risk management and planning procedures which integrate current practices. This was done through the CEDA Archival Format Audit which inspected British Atmospheric Data Centre and NERC Earth Observation Data Centre Archival holdings. These holdings are extensive, comprising of around 2 Petabytes of data and 137 million individual files, which were analysed and characterised in terms of format, based risk. We are then able to present an overview of the format based risk burden faced by a large scale archive attempting to maintain the usability of heterogeneous environmental data sets We continue by presenting a dynamic data management information model and provide discussion of the following core model entities and their relationships: Aspirational entities, which include Data Entity definitions and their associated Preservation Objectives. Risk entities, which act as drivers for change within the data lifecycle. These include Acquisitional Risks, Technical Risks, Strategic Risks and External Risks Plan entities, which detail the actions to bring about change within an archive. These include Acquisition Plans, Preservation Plans and Monitoring plans which support responsive interactions with the community. The Result entities describe the outcomes of the plans. This includes Acquisitions. Mitigations and Accepted Risks. With risk acceptance permitting imperfect but functional solutions that can be realistically supported within an archives resource levels

Wyoming Landscape Conservation Initiative data management and integration

USGS Publications Warehouse

Latysh, Natalie; Bristol, R. Sky

2011-01-01

Six Federal agencies, two State agencies, and two local entities formally support the Wyoming Landscape Conservation Initiative (WLCI) and work together on a landscape scale to manage fragile habitats and wildlife resources amidst growing energy development in southwest Wyoming. The U.S. Geological Survey (USGS) was tasked with implementing targeted research and providing scientific information about southwest Wyoming to inform the development of WLCI habitat enhancement and restoration projects conducted by land management agencies. Many WLCI researchers and decisionmakers representing the Bureau of Land Management, U.S. Fish and Wildlife Service, the State of Wyoming, and others have overwhelmingly expressed the need for a stable, robust infrastructure to promote sharing of data resources produced by multiple entities, including metadata adequately describing the datasets. Descriptive metadata facilitates use of the datasets by users unfamiliar with the data. Agency representatives advocate development of common data handling and distribution practices among WLCI partners to enhance availability of comprehensive and diverse data resources for use in scientific analyses and resource management. The USGS Core Science Informatics (CSI) team is developing and promoting data integration tools and techniques across USGS and partner entity endeavors, including a data management infrastructure to aid WLCI researchers and decisionmakers.

MRI findings in acute hyperammonemic encephalopathy resulting from decompensated chronic liver disease.

PubMed

Sureka, Jyoti; Jakkani, Ravi Kanth; Panwar, Sanuj

2012-06-01

Hyperammonemic encephalopathy is a type of metabolic encephalopathy with diversified etiology. Hyperammonemia is the end result of several metabolic disorders such as congenital deficiencies of urea cycle enzymes, hepatic encephalopathy, Reye's syndrome and other toxic encephalopathies. Non-specific clinical presentation poses a great challenge in early diagnosis of this entity. Irrespective of the underlying etiology, hyperammonemia causes a distinctive pattern of brain parenchymal injury. The cingulate gyrus and insular cortex are more vulnerable to this type of toxic insult. Characteristic magnetic resonance imaging findings in combination with laboratory parameters can help to differentiate this entity from other metabolic encephalopathy and thus aiding in early diagnosis and treatment.

Apoptosis and apoptotic pathway in actinic prurigo by immunohistochemistry

PubMed Central

Cuevas-González, Juan-Carlos; García-Vázquez, Francisco-Javier; Rodríguez-Lobato, Erika; Farfán-Morales, José-Eduardo

2016-01-01

Background Actinic prurigo (AP) is an idiopathic photodermatosis, this entity requires exposure to UV-B and -A to develop lesions. Apoptosis is a physiological death program that can be initiated by a permanently active mechanism (extrinsic pathway) or irreparable damage (intrinsic pathway). Material and Methods Descriptive study, the sample size comprised 64 paraffin blocks of tissue with a diagnosis of AP. In H&E-stained slides, the diagnosis of AP was corroborated, and 1-µm-thick sections were processed for immunohistochemistry (IHC). A database was constructed with SPSS version 20, Inc., Chicago, IL, USA, and descriptive statistics were analyzed by X2 test and comparison of means. Results A total of 64 cases were processed, of which 40 (62.5%) were cheilitis AP and 24 (37.5%) were AP in the skin. Of the 40 cheilitis samples, 27 were positive for Bcl-2 and caspase 3 (67.5%), p53 was expressed in 30 (75%). Of the skin lesions,p53 and caspase 3 were expressed in 18 of 24 cases (75%), and 13 were positive for Bcl-2 (54%). Conclusions We propose that apoptosis is the last step in the type IV subtype a-b hypersensitivity response-activation of the intrinsic pathway indicates that external factors, such as UV-A and -B are the trigger. Key words:Apoptosis, actinic prurigo, cheilitis actinic prurigo. PMID:26615506

[Main malignant neoplasms in Mexico and their geographic distribution, 1993-2002].

PubMed

Meneses-García, Abelardo; Ruiz-Godoy, Luz María; Beltrán-Ortega, Arturo; Sánchez-Cervantes, Felipe; Tapia-Conyer, Roberto; Mohar, Alejandro

2012-01-01

INTRODUCCION: Cancer is one of the main causes of death worldwide. In Mexico it represents the third cause of death. OBJECTIVE. To know the frequency and distribution of the malignancies diagnosed in Mexico during 10 years. From the data-base of the histopathological register of malignant neoplasms in Mexico, was obtained a descriptive analysis from the period 1993-2002. The variables included were: city and federative entity of residence, age, sex, anatomical region and histopathologic diagnosis. From the 12 more common malignant neoplasms a descriptive demographic analysis was performed adjusted by four regions: Center, North, South and Federal District. A total of 767,464 cases with cancer were reported. In order of frequency were: cervix-uterine cancer, breast cancer, prostate cancer, lymphomas, colorectal cancer, gastric cancer, sarcomas, ovary cancer, lung cancer, leukemias, urinary bladder cancer and uterine body. Seventy-two percent were diagnosed in women and 28% in men, the reason for a ratio W:M of 2.5:1. The states more developed and industrialized, near to United States had the majority of cases from breast, prostate, ovary and lung cancer. There is a distinctive distribution type of malignant tumors in Mexico, according to the region of residence. It absolutely is necessary to developed population based cancer registries. These are the best instruments to better understand the magnitude of cancer, and evaluate incidence, survival and mortality.

Efficient authentication scheme based on near-ring root extraction problem

NASA Astrophysics Data System (ADS)

Muthukumaran, V.; Ezhilmaran, D.

2017-11-01

An authentication protocolis the type of computer communication protocol or cryptography protocol specifically designed for transfer of authentication data between two entities. We have planned a two new entity authentication scheme on the basis of root extraction problem near-ring in this article. We suggest that this problem is suitably difficult to serve as a cryptographic assumption over the platform of near-ring N. The security issues also discussed.

MediaNet: a multimedia information network for knowledge representation

NASA Astrophysics Data System (ADS)

Benitez, Ana B.; Smith, John R.; Chang, Shih-Fu

2000-10-01

In this paper, we present MediaNet, which is a knowledge representation framework that uses multimedia content for representing semantic and perceptual information. The main components of MediaNet include conceptual entities, which correspond to real world objects, and relationships among concepts. MediaNet allows the concepts and relationships to be defined or exemplified by multimedia content such as images, video, audio, graphics, and text. MediaNet models the traditional relationship types such as generalization and aggregation but adds additional functionality by modeling perceptual relationships based on feature similarity. For example, MediaNet allows a concept such as car to be defined as a type of a transportation vehicle, but which is further defined and illustrated through example images, videos and sounds of cars. In constructing the MediaNet framework, we have built on the basic principles of semiotics and semantic networks in addition to utilizing the audio-visual content description framework being developed as part of the MPEG-7 multimedia content description standard. By integrating both conceptual and perceptual representations of knowledge, MediaNet has potential to impact a broad range of applications that deal with multimedia content at the semantic and perceptual levels. In particular, we have found that MediaNet can improve the performance of multimedia retrieval applications by using query expansion, refinement and translation across multiple content modalities. In this paper, we report on experiments that use MediaNet in searching for images. We construct the MediaNet knowledge base using both WordNet and an image network built from multiple example images and extracted color and texture descriptors. Initial experimental results demonstrate improved retrieval effectiveness using MediaNet in a content-based retrieval system.

Interobserver reproducibility in pathologist interpretation of columnar-lined esophagus.

PubMed

Mastracci, Luca; Piol, Nataniele; Molinaro, Luca; Pitto, Francesca; Tinelli, Carmine; De Silvestri, Annalisa; Fiocca, Roberto; Grillo, Federica

2016-02-01

Confirmation of endoscopically suspected esophageal metaplasia (ESEM) requires histology, but confusion in the histological definition of columnar-lined esophagus (CLE) is a longstanding problem. The aim of this study is to evaluate interpathologist variability in the interpretation of CLE. Thirty pathologists were invited to review three ten-case sets of CLE biopsies. In the first set, the cases were provided with descriptive endoscopy only; in the second and the third sets, ESEM extent using Prague criteria was provided. Moreover, participants were required to refer to a diagnostic chart for evaluation of the third set. Agreement was statistically assessed using Randolph's free-marginal multirater kappa. While substantial agreement in recognizing columnar epithelium (K = 0.76) was recorded, the overall concordance in clinico-pathological diagnosis was low (K = 0.38). The overall concordance rate improved from the first (K = 0.27) to the second (K = 0.40) and third step (K = 0.46). Agreement was substantial when diagnosing Barrett's esophagus (BE) with intestinal metaplasia or inlet patch (K = 0.65 and K = 0.89), respectively, in the third step, while major problems in interpretation of CLE were observed when only cardia/cardia-oxyntic atrophic-type epithelium was present (K = 0.05-0.29). In conclusion, precise endoscopic description and the use of a diagnostic chart increased consistency in CLE interpretation of esophageal biopsies. Agreement was substantial for some diagnostic categories (BE with intestinal metaplasia and inlet patch) with a well-defined clinical profile. Interpretation of cases with cardia/cardia-oxyntic atrophic-type epithelium, with or without ESEM, was least consistent, which reflects lack of clarity of definition and results in variable management of this entity.

Dementia and cognitive decline in type 2 diabetes and prediabetic stages: towards targeted interventions.

PubMed

Biessels, Geert Jan; Strachan, Mark W J; Visseren, Frank L J; Kappelle, L Jaap; Whitmer, Rachel A

2014-03-01

Type 2 diabetes is associated with dementia, and also with more slight cognitive decrements. In this Review we discuss trajectories from normal cognition to dementia in people with type 2 diabetes, and explore opportunities for treatment. Slight diabetes-associated cognitive decrements and dementia affect different age groups and show a different evolution. These cognitive entities should therefore not be regarded as a continuum, although their effects might be additive. Vascular damage is a key underlying process in both entities. Glucose-mediated processes and other metabolic disturbances might also have a role. No treatment has been established, but management of vascular risk factors and optimisation of glycaemic control could have therapeutic benefit. We identify possible opportunities for intervention to improve cognitive outcomes in people with type 2 diabetes, and suggest how treatment can be tailored to individual risk profiles and comorbidities. Copyright © 2014 Elsevier Ltd. All rights reserved.

Constructing Topic Models of Internet of Things for Information Processing

PubMed Central

Xin, Jie; Cui, Zhiming; Zhang, Shukui; He, Tianxu; Li, Chunhua; Huang, Haojing

2014-01-01

Internet of Things (IoT) is regarded as a remarkable development of the modern information technology. There is abundant digital products data on the IoT, linking with multiple types of objects/entities. Those associated entities carry rich information and usually in the form of query records. Therefore, constructing high quality topic hierarchies that can capture the term distribution of each product record enables us to better understand users' search intent and benefits tasks such as taxonomy construction, recommendation systems, and other communications solutions for the future IoT. In this paper, we propose a novel record entity topic model (RETM) for IoT environment that is associated with a set of entities and records and a Gibbs sampling-based algorithm is proposed to learn the model. We conduct extensive experiments on real-world datasets and compare our approach with existing methods to demonstrate the advantage of our approach. PMID:25110737

Constructing topic models of Internet of Things for information processing.

PubMed

Xin, Jie; Cui, Zhiming; Zhang, Shukui; He, Tianxu; Li, Chunhua; Huang, Haojing

2014-01-01

Internet of Things (IoT) is regarded as a remarkable development of the modern information technology. There is abundant digital products data on the IoT, linking with multiple types of objects/entities. Those associated entities carry rich information and usually in the form of query records. Therefore, constructing high quality topic hierarchies that can capture the term distribution of each product record enables us to better understand users' search intent and benefits tasks such as taxonomy construction, recommendation systems, and other communications solutions for the future IoT. In this paper, we propose a novel record entity topic model (RETM) for IoT environment that is associated with a set of entities and records and a Gibbs sampling-based algorithm is proposed to learn the model. We conduct extensive experiments on real-world datasets and compare our approach with existing methods to demonstrate the advantage of our approach.

Next level of board accountability in health care quality.

PubMed

Pronovost, Peter J; Armstrong, C Michael; Demski, Renee; Peterson, Ronald R; Rothman, Paul B

2018-03-19

Purpose The purpose of this paper is to offer six principles that health system leaders can apply to establish a governance and management system for the quality of care and patient safety. Design/methodology/approach Leaders of a large academic health system set a goal of high reliability and formed a quality board committee in 2011 to oversee quality and patient safety everywhere care was delivered. Leaders of the health system and every entity, including inpatient hospitals, home care companies, and ambulatory services staff the committee. The committee works with the management for each entity to set and achieve quality goals. Through this work, the six principles emerged to address management structures and processes. Findings The principles are: ensure there is oversight for quality everywhere care is delivered under the health system; create a framework to organize and report the work; identify care areas where quality is ambiguous or underdeveloped (i.e. islands of quality) and work to ensure there is reporting and accountability for quality measures; create a consolidated quality statement similar to a financial statement; ensure the integrity of the data used to measure and report quality and safety performance; and transparently report performance and create an explicit accountability model. Originality/value This governance and management system for quality and safety functions similar to a finance system, with quality performance documented and reported, data integrity monitored, and accountability for performance from board to bedside. To the authors' knowledge, this is the first description of how a board has taken this type of systematic approach to oversee the quality of care.

Vantage Construal in the Attributive Use of Basic Color Terms: The A[subscript C]N and N of N[subscript C] Constructions

ERIC Educational Resources Information Center

Anishchanka, Alena

2010-01-01

The article presents a usage-based analysis of color attribution, i.e. the construal of the relation between color property and an entity to which it is attributed in painting descriptions. The study is based on the corpus of 100 catalog entries written for American art museums. It focuses on the two most frequent morpho-syntactic patterns in the…

Public Safety Broadband Network Architecture Description

DTIC Science & Technology

2013-08-01

could be used to add an in-app purchase to the user’s mobile phone bill. Major operators , such as AT& T , Deutsche Telekom, Orange, Telefonica and...3GPP technologies such as CDMA2000 and WiMAX networks. MME Mobility Managemen t Entity The MME is the key control-node for the LTE access-network... operator ( operator -managed small cells, etc.) or provides sufficient security (authentication, encryption, etc.). See Figure D3. Figure D3: ITU- T

Loin Pain Haematuria Syndrome - A Narrative Review of Pain Management Strategies

PubMed Central

2016-01-01

Loin pain haematuria syndrome (LPHS) is an uncommon clinical entity that has divided renal physicians, pain practitioners, and even psychiatrists since its initial description. A relative paucity of data exists regarding the condition, with best practice guidelines lacking amid the existing threads of anecdotal experiences and variable follow-up observations. The aim of this article was to review the cumulative published experience of pain relief strategies for LPHS. PMID:27103962

Quantum epistemology from subquantum ontology: Quantum mechanics from theory of classical random fields

NASA Astrophysics Data System (ADS)

Khrennikov, Andrei

2017-02-01

The scientific methodology based on two descriptive levels, ontic (reality as it is) and epistemic (observational), is briefly presented. Following Schrödinger, we point to the possible gap between these two descriptions. Our main aim is to show that, although ontic entities may be unaccessible for observations, they can be useful for clarification of the physical nature of operational epistemic entities. We illustrate this thesis by the concrete example: starting with the concrete ontic model preceding quantum mechanics (the latter is treated as an epistemic model), namely, prequantum classical statistical field theory (PCSFT), we propose the natural physical interpretation for the basic quantum mechanical entity-the quantum state ("wave function"). The correspondence PCSFT ↦ QM is not straightforward, it couples the covariance operators of classical (prequantum) random fields with the quantum density operators. We use this correspondence to clarify the physical meaning of the pure quantum state and the superposition principle-by using the formalism of classical field correlations. In classical mechanics the phase space description can be considered as the ontic description, here states are given by points λ =(x , p) of phase space. The dynamics of the ontic state is given by the system of Hamiltonian equations.We can also consider probability distributions on the phase space (or equivalently random variables valued in it). We call them probabilistic ontic states. Dynamics of probabilistic ontic states is given by the Liouville equation.In classical physics we can (at least in principle) measure both the coordinate and momentum and hence ontic states can be treated as epistemic states as well (or it is better to say that here epistemic states can be treated as ontic states). Probabilistic ontic states represent probabilities for outcomes of joint measurement of position and momentum.However, this was a very special, although very important, example of description of physical phenomena. In general there are no reasons to expect that properties of ontic states are approachable through our measurements. There is a gap between ontic and epistemic descriptions, cf. also with 't Hooft [49,50] and G G. Groessing et al. [51]. In general the presence of such a gap also implies unapproachability of the probabilistic ontic states, i.e., probability distributions on the space of ontic states. De Broglie [28] called such probability distributions hidden probabilities and distinguished them sharply from probability distributions of measurements outcomes, see also Lochak [29]. (The latter distributions are described by the quantum formalism.)This ontic-epistemic approach based on the combination of two descriptive levels for natural phenomena is closely related to the old Bild conception which was originated in the works of Hertz. Later it was heavily explored by Schrödinger in the quantum domain, see, e.g., [8,11] for detailed analysis. According to Hertz one cannot expect to construct a complete theoretical model based explicitly on observable quantities. The complete theoretical model can contain quantities which are unapproachable for external measurement inspection. For example, Hertz by trying to create a mechanical model for Maxwell's electromagnetism invented hidden masses. The main distinguishing property of a theoretical model (in contrast to an observational model) is the continuity of description, i.e., the absence of gaps in description. From this viewpoint, the quantum mechanical description is not continuous: there is a gap between premeasurement dynamics and the measurement outcome. QM cannot say anything what happens in the process of measurement, this is the well known measurement problem of QM [32], cf. [52,53]. Continuity of description is closely related to causality. However, here we cannot go in more detail, see [8,11].The important question is about interrelation between two levels of description, ontic-epistemic (or theoretical-observational). In the introduction we have already cited Schrödinger who emphasized the possible complexity of this interrelation. In particular, in general there is no reason to expect a straightforward coupling of the form, cf. [9,10]:

PKDE4J: Entity and relation extraction for public knowledge discovery.

PubMed

Song, Min; Kim, Won Chul; Lee, Dahee; Heo, Go Eun; Kang, Keun Young

2015-10-01

Due to an enormous number of scientific publications that cannot be handled manually, there is a rising interest in text-mining techniques for automated information extraction, especially in the biomedical field. Such techniques provide effective means of information search, knowledge discovery, and hypothesis generation. Most previous studies have primarily focused on the design and performance improvement of either named entity recognition or relation extraction. In this paper, we present PKDE4J, a comprehensive text-mining system that integrates dictionary-based entity extraction and rule-based relation extraction in a highly flexible and extensible framework. Starting with the Stanford CoreNLP, we developed the system to cope with multiple types of entities and relations. The system also has fairly good performance in terms of accuracy as well as the ability to configure text-processing components. We demonstrate its competitive performance by evaluating it on many corpora and found that it surpasses existing systems with average F-measures of 85% for entity extraction and 81% for relation extraction. Copyright © 2015 Elsevier Inc. All rights reserved.

Technology development: A partnership that makes sense

NASA Technical Reports Server (NTRS)

Rone, Kyle Y.; Macdonald, Robert B.; Houston, A. Glen

1991-01-01

Discussed here is an approach to how academic institutions, government entities, and industrial organizations can work effectively to utilize their relative strengths to more effectively meet common goals. The discussion relates to the University of Houston-Clear Lake (UHCL) Research Institute for Computing and Information Systems (RICIS) Program to bring about this type of triad in the Clear Lake area. It is concluded that the interfaces among these groups must remain independent to maintain a healthy counterbalance to their respective entities. However, each entity can and must understand the entire mechanism to exploit each interface to the fullest. Only through such cooperation can the continued technical success of the NASA/Clear Lake area be assured.

A New (Type 3) Prophage of “Candidatus Liberibacter asiaticus” in China

USDA-ARS?s Scientific Manuscript database

Prophages are important genetic entities of “Candidatus Liberibacter asiaticus” (CLas), a non-culturable a-proteobacterium associated with citrus Huanglongbing (HLB). Two CLas prophages have been described, SC1 (NC_019549.1, Type 1) and SC2 (NC_019550.1, Type 2). To explore the prophage repertoire, ...

A case of adult anaplastic cerebellar ganglioglioma

PubMed Central

Bouali, Sofiene; Maatar, Nidhal; Zehani, Alia; Mahmoud, Maha; Kallel, Jalel; Jemel, Hafedh

2018-01-01

Background: Anaplastic posterior fossa ganglioglioma in adults is exceedingly rare. To date, only one case of adult anaplastic posterior fossa ganglioglioma has been reported in the English literature and none has been described at the cerebellum. To our knowledge, this report is the third case of malignant posterior fossa ganglioglioma in adults and the first at the cerebellum. In general, this entity can be misdiagnosed preoperatively as a primary posterior fossa neoplasm, and by reporting our clinical and radiographic observations we want to add to the existing literature on this rare entity. Case Description: A 40-year-old man presented with a history of headaches and dizziness and progressive gait disturbance and was diagnosed with anaplastic ganglioglioma in the posterior fossa. Conclusions: Although rare, our case demonstrates that anaplastic ganglioglioma should be considered in the differential diagnosis of infratentorial tumors in adult patients. PMID:29527389

[Pneumomediastinum, giant subcutaneous emphysema and pneumoperitoneum revealed by jaw pain. Uncommon physiopathology of pneumomediastinum].

PubMed

Le Loch, J-B; Freymond, N; Khettab, F; Pacheco, Y; Devouassoux, G

2008-02-01

Spontaneous pneumomediastinum is a rare entity, predominantly described in young man. The association of acute dyspnea, chest pains and subcutaneous emphysema is usually reported. We report the observation of a pneumomediastinum, fortuitously discovered in front of an isolated giant subcutaneous emphysema in a 59 year old man. The recent clinical history was only marked by the presence of intense and acute dental pains. Associated with a pneumoperitoneum, a retro-pneumoperitoneum, this clinical presentation is uncommon and differs from previous published case reports. Despite a complete evaluation of classical risk factors, its origin remains uncertain. However, the presence of huge dental injuries led to consider such local origin, facilitating air diffusion. This case report allows to reconsider spontaneous pneumomediastinum entity and to propose additional physiopathological mechanisms. This original description underlines the interest to systematically perform dental examination in the presence of unexplained pneumomediastinum.

A description of rotations for DEM models of particle systems

NASA Astrophysics Data System (ADS)

Campello, Eduardo M. B.

2015-06-01

In this work, we show how a vector parameterization of rotations can be adopted to describe the rotational motion of particles within the framework of the discrete element method (DEM). It is based on the use of a special rotation vector, called Rodrigues rotation vector, and accounts for finite rotations in a fully exact manner. The use of fictitious entities such as quaternions or complicated structures such as Euler angles is thereby circumvented. As an additional advantage, stick-slip friction models with inter-particle rolling motion are made possible in a consistent and elegant way. A few examples are provided to illustrate the applicability of the scheme. We believe that simple vector descriptions of rotations are very useful for DEM models of particle systems.

Hybrid approaches for multiple-species stochastic reaction–diffusion models

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

Spill, Fabian, E-mail: fspill@bu.edu; Department of Mechanical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139; Guerrero, Pilar

2015-10-15

Reaction–diffusion models are used to describe systems in fields as diverse as physics, chemistry, ecology and biology. The fundamental quantities in such models are individual entities such as atoms and molecules, bacteria, cells or animals, which move and/or react in a stochastic manner. If the number of entities is large, accounting for each individual is inefficient, and often partial differential equation (PDE) models are used in which the stochastic behaviour of individuals is replaced by a description of the averaged, or mean behaviour of the system. In some situations the number of individuals is large in certain regions and smallmore » in others. In such cases, a stochastic model may be inefficient in one region, and a PDE model inaccurate in another. To overcome this problem, we develop a scheme which couples a stochastic reaction–diffusion system in one part of the domain with its mean field analogue, i.e. a discretised PDE model, in the other part of the domain. The interface in between the two domains occupies exactly one lattice site and is chosen such that the mean field description is still accurate there. In this way errors due to the flux between the domains are small. Our scheme can account for multiple dynamic interfaces separating multiple stochastic and deterministic domains, and the coupling between the domains conserves the total number of particles. The method preserves stochastic features such as extinction not observable in the mean field description, and is significantly faster to simulate on a computer than the pure stochastic model. - Highlights: • A novel hybrid stochastic/deterministic reaction–diffusion simulation method is given. • Can massively speed up stochastic simulations while preserving stochastic effects. • Can handle multiple reacting species. • Can handle moving boundaries.« less

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

PubMed Central

Kerrien, Samuel; Orchard, Sandra; Montecchi-Palazzi, Luisa; Aranda, Bruno; Quinn, Antony F; Vinod, Nisha; Bader, Gary D; Xenarios, Ioannis; Wojcik, Jérôme; Sherman, David; Tyers, Mike; Salama, John J; Moore, Susan; Ceol, Arnaud; Chatr-aryamontri, Andrew; Oesterheld, Matthias; Stümpflen, Volker; Salwinski, Lukasz; Nerothin, Jason; Cerami, Ethan; Cusick, Michael E; Vidal, Marc; Gilson, Michael; Armstrong, John; Woollard, Peter; Hogue, Christopher; Eisenberg, David; Cesareni, Gianni; Apweiler, Rolf; Hermjakob, Henning

2007-01-01

Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. Results The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. Conclusion The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel. PMID:17925023

Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology

PubMed Central

Vogt, Lars; Grobe, Peter; Quast, Björn; Bartolomaeus, Thomas

2011-01-01

Background Application oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO) is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them. Methodology/Principal Findings By systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: ‘fiat object part aggregate’ and ‘object with fiat object part aggregate’. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity. Conclusions/Significance We suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of material entity that application oriented ontologies may use as templates. Our result, however, depends on the premise that all material entities are organized according to a constitutive granularity. PMID:21533043

High Grade Serous Cystadenocarcinoma of Testis-Case Report of a Rare Ovarian Epithelial Type Tumour

PubMed Central

Nayanar, Sangeetha K; Varadharajaperumal, R; Satheeshbabu, TV; Balasubramanian, Satheesan

2017-01-01

Ovarian epithelial type tumour of testis are extremely rare tumours that resemble ovarian surface epithelial tumours. They usually present as testicular or paratesticular tumours and can be serous, mucinous, endometrioid or Brenner tumour. Serous and mucinous types account for the majority of tumours. The tumours are benign, borderline or malignant, commonly borderline. Here, we report a case of high grade serous cyst adenocarcinoma of testis which manifested as extensive metastasis in supraclavicular, mediastinal and abdominopelvic groups of lymph nodes, lung and adrenal gland without clinical evidence of an overt primary tumour. We report this case so as to make clinicians and pathologists aware of this rare entity and to stress on the fact that this rare entity should be kept in mind when evaluating cases of metastatic adenocarcinoma in male patients. PMID:28764180

Atrophia maculosa varioliformis cutis. Report of two cases and review of the literature.

PubMed

Kolenik, S A; Perez, M I; Davidson, D M; Morganroth, G S; Kohn, S R; Bolognia, J L

1994-05-01

Atrophia maculosa varioliformis cutis was initially described in 1918 as an entity in which both linear and punctate scars appeared spontaneously on normal facial skin. To the best of our knowledge, only five additional cases have been described. We describe two patients, 14 and 20 years of age, whose histories and clinical lesions fit the description of atrophia maculosa varioliformis cutis. The histologic findings are also described, and the literature to date is reviewed.

NASA printing, duplicating, and copying management handbook

NASA Technical Reports Server (NTRS)

1993-01-01

This handbook provides information and procedures for the implementation of NASA policy and applicable laws and regulations relating to printing, duplicating, and copying. The topics addressed include a description of relevant laws and regulations, authorizations required, and responsible entities for NASA printing, duplicating, and copying. The policy of NASA is to ensure understanding and application of authority and responsibility on printing matters. Where necessary, the handbook clarifies the intent of basic laws and regulations applicable to NASA.

Clinical Relation Extraction Toward Drug Safety Surveillance Using Electronic Health Record Narratives: Classical Learning Versus Deep Learning.

PubMed

Munkhdalai, Tsendsuren; Liu, Feifan; Yu, Hong

2018-04-25

Medication and adverse drug event (ADE) information extracted from electronic health record (EHR) notes can be a rich resource for drug safety surveillance. Existing observational studies have mainly relied on structured EHR data to obtain ADE information; however, ADEs are often buried in the EHR narratives and not recorded in structured data. To unlock ADE-related information from EHR narratives, there is a need to extract relevant entities and identify relations among them. In this study, we focus on relation identification. This study aimed to evaluate natural language processing and machine learning approaches using the expert-annotated medical entities and relations in the context of drug safety surveillance, and investigate how different learning approaches perform under different configurations. We have manually annotated 791 EHR notes with 9 named entities (eg, medication, indication, severity, and ADEs) and 7 different types of relations (eg, medication-dosage, medication-ADE, and severity-ADE). Then, we explored 3 supervised machine learning systems for relation identification: (1) a support vector machines (SVM) system, (2) an end-to-end deep neural network system, and (3) a supervised descriptive rule induction baseline system. For the neural network system, we exploited the state-of-the-art recurrent neural network (RNN) and attention models. We report the performance by macro-averaged precision, recall, and F1-score across the relation types. Our results show that the SVM model achieved the best average F1-score of 89.1% on test data, outperforming the long short-term memory (LSTM) model with attention (F1-score of 65.72%) as well as the rule induction baseline system (F1-score of 7.47%) by a large margin. The bidirectional LSTM model with attention achieved the best performance among different RNN models. With the inclusion of additional features in the LSTM model, its performance can be boosted to an average F1-score of 77.35%. It shows that classical learning models (SVM) remains advantageous over deep learning models (RNN variants) for clinical relation identification, especially for long-distance intersentential relations. However, RNNs demonstrate a great potential of significant improvement if more training data become available. Our work is an important step toward mining EHRs to improve the efficacy of drug safety surveillance. Most importantly, the annotated data used in this study will be made publicly available, which will further promote drug safety research in the community. ©Tsendsuren Munkhdalai, Feifan Liu, Hong Yu. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 25.04.2018.

Clinical Relation Extraction Toward Drug Safety Surveillance Using Electronic Health Record Narratives: Classical Learning Versus Deep Learning

PubMed Central

Munkhdalai, Tsendsuren; Liu, Feifan

2018-01-01

Background Medication and adverse drug event (ADE) information extracted from electronic health record (EHR) notes can be a rich resource for drug safety surveillance. Existing observational studies have mainly relied on structured EHR data to obtain ADE information; however, ADEs are often buried in the EHR narratives and not recorded in structured data. Objective To unlock ADE-related information from EHR narratives, there is a need to extract relevant entities and identify relations among them. In this study, we focus on relation identification. This study aimed to evaluate natural language processing and machine learning approaches using the expert-annotated medical entities and relations in the context of drug safety surveillance, and investigate how different learning approaches perform under different configurations. Methods We have manually annotated 791 EHR notes with 9 named entities (eg, medication, indication, severity, and ADEs) and 7 different types of relations (eg, medication-dosage, medication-ADE, and severity-ADE). Then, we explored 3 supervised machine learning systems for relation identification: (1) a support vector machines (SVM) system, (2) an end-to-end deep neural network system, and (3) a supervised descriptive rule induction baseline system. For the neural network system, we exploited the state-of-the-art recurrent neural network (RNN) and attention models. We report the performance by macro-averaged precision, recall, and F1-score across the relation types. Results Our results show that the SVM model achieved the best average F1-score of 89.1% on test data, outperforming the long short-term memory (LSTM) model with attention (F1-score of 65.72%) as well as the rule induction baseline system (F1-score of 7.47%) by a large margin. The bidirectional LSTM model with attention achieved the best performance among different RNN models. With the inclusion of additional features in the LSTM model, its performance can be boosted to an average F1-score of 77.35%. Conclusions It shows that classical learning models (SVM) remains advantageous over deep learning models (RNN variants) for clinical relation identification, especially for long-distance intersentential relations. However, RNNs demonstrate a great potential of significant improvement if more training data become available. Our work is an important step toward mining EHRs to improve the efficacy of drug safety surveillance. Most importantly, the annotated data used in this study will be made publicly available, which will further promote drug safety research in the community. PMID:29695376

Implementation of the Zuluaga-Raysmith (Z-R) model for assessment of perceived basic human needs in home health clients and caregivers.

PubMed

Zuluaga, B H

2000-01-01

The Zuluaga-Raysmith (Z-R) model is a conceptual framework that incorporates accepted concepts of universal basic human needs developed by Maslow, yet removes the hierarchical nature of these. The Z-R model recognizes the existence of a health-illness continuum and accepts that an entity (individual, family, aggregate, or community) may move freely in the direction of greater health and self-actualization or towards illness and premature death. The Z-R model identifies 10 basic needs and recognizes that a perceived deficit in any one of these needs can adversely affect the level of wellness of the entity being considered. This exploratory and descriptive study used 11 nurses as interviewers. Subjects consisted of a convenience sample of homebound clients of a home health agency in a metropolitan city, and selected caregivers (n = 27). A modified functional wellness inventory (developed in 1993 by Louvenia Carter) was used with several open-ended questions, which together related to the 10 needs of the Z-R model. Reliability coefficient of the instrument was 0.84. Descriptive statistics were used to analyze the data, using means, percentages, and frequencies. Open-ended questions were grouped according to content and ranked in order of frequency. The five most pressing needs of this small sample were income; physical health; opportunity to make a contribution; mobility; and mental, emotional, social, and spiritual health (MESSH). Nurses unanimously reported that use of the instrument and the Z-R model helped them to focus on the total person, identify strengths in their clients, identify perceived needs deficits, and therefore, with the client, facilitate the preparation of a timely and cost-effective interdisciplinary plan of care to help the entity to move to a higher level of wellness despite the presence of chronic disease, disability, or impending death. These findings suggested that further research is warranted to explore the use of the Z-R model. A replication study is in progress.

C2 Product-Centric Approach to Transforming Current C4ISR Information Architectures

DTIC Science & Technology

2004-06-01

each type of environment . For “Cultural Feature” Entity Kind only the “Land” Domain is defined and for “ Environmental ” Entity Kind only the...take advantage of both worlds. In particular, the unifying concept of a Model-Driven Architecture (MDA) under development by the Object Management...Exchange Requirements (IER) to an XML environment . FCS [4] developers have embraced both UML and XML for their architectures and MIP [5] too is migrating

Pre-incident Analysis using Multigraphs and Faceted Ontologies

DTIC Science & Technology

2013-08-01

ontology for beverages, part of which is shown in the form of an entity- relationship (ER) graph in Figure 4. The entities Beer , Wine, etc. have is a...another from Beer to Grains. The terminology is suggestive: The is a type of link has already been defined (informally). The made from link...expressions derived from natural language such as Beer , is a, Grains and made from. Labels alone are insufficient for a computer system for ontology and

Mayo Clinic/Renal Pathology Society Consensus Report on Pathologic Classification, Diagnosis, and Reporting of GN.

PubMed

Sethi, Sanjeev; Haas, Mark; Markowitz, Glen S; D'Agati, Vivette D; Rennke, Helmut G; Jennette, J Charles; Bajema, Ingeborg M; Alpers, Charles E; Chang, Anthony; Cornell, Lynn D; Cosio, Fernando G; Fogo, Agnes B; Glassock, Richard J; Hariharan, Sundaram; Kambham, Neeraja; Lager, Donna J; Leung, Nelson; Mengel, Michael; Nath, Karl A; Roberts, Ian S; Rovin, Brad H; Seshan, Surya V; Smith, Richard J H; Walker, Patrick D; Winearls, Christopher G; Appel, Gerald B; Alexander, Mariam P; Cattran, Daniel C; Casado, Carmen Avila; Cook, H Terence; De Vriese, An S; Radhakrishnan, Jai; Racusen, Lorraine C; Ronco, Pierre; Fervenza, Fernando C

2016-05-01

Renal pathologists and nephrologists met on February 20, 2015 to establish an etiology/pathogenesis-based system for classification and diagnosis of GN, with a major aim of standardizing the kidney biopsy report of GN. On the basis of etiology/pathogenesis, GN is classified into the following five pathogenic types, each with specific disease entities: immune-complex GN, pauci-immune GN, antiglomerular basement membrane GN, monoclonal Ig GN, and C3 glomerulopathy. The pathogenesis-based classification forms the basis of the kidney biopsy report. To standardize the report, the diagnosis consists of a primary diagnosis and a secondary diagnosis. The primary diagnosis should include the disease entity/pathogenic type (if disease entity is not known) followed in order by pattern of injury (mixed patterns may be present); score/grade/class for disease entities, such as IgA nephropathy, lupus nephritis, and ANCA GN; and additional features as detailed herein. A pattern diagnosis as the sole primary diagnosis is not recommended. Secondary diagnoses should be reported separately and include coexisting lesions that do not form the primary diagnosis. Guidelines for the report format, light microscopy, immunofluorescence microscopy, electron microscopy, and ancillary studies are also provided. In summary, this consensus report emphasizes a pathogenesis-based classification of GN and provides guidelines for the standardized reporting of GN. Copyright © 2016 by the American Society of Nephrology.

A versatile petri net based architecture for modeling and simulation of complex biological processes.

PubMed

Nagasaki, Masao; Doi, Atsushi; Matsuno, Hiroshi; Miyano, Satoru

2004-01-01

The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process of modeling metabolic, gene regulatory or signal transduction pathways with the architecture, we have realized three extensions of HFPN, (i) an entity should be extended to contain more than one value, (ii) an entity should be extended to handle other primitive types, e.g. boolean, string, (iii) an entity should be extended to handle more advanced type called object that consists of variables and methods, are necessary for modeling biological systems with Petri net based architecture. To deal with it, we define a new enhanced Petri net called hybrid functional Petri net with extension (HFPNe). To demonstrate the effectiveness of the enhancements, we model and simulate with HFPNe four biological processes that are diffcult to represent with the previous architecture HFPN.

Building a protein name dictionary from full text: a machine learning term extraction approach.

PubMed

Shi, Lei; Campagne, Fabien

2005-04-07

The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt.

Building a protein name dictionary from full text: a machine learning term extraction approach

PubMed Central

Shi, Lei; Campagne, Fabien

2005-01-01

Background The majority of information in the biological literature resides in full text articles, instead of abstracts. Yet, abstracts remain the focus of many publicly available literature data mining tools. Most literature mining tools rely on pre-existing lexicons of biological names, often extracted from curated gene or protein databases. This is a limitation, because such databases have low coverage of the many name variants which are used to refer to biological entities in the literature. Results We present an approach to recognize named entities in full text. The approach collects high frequency terms in an article, and uses support vector machines (SVM) to identify biological entity names. It is also computationally efficient and robust to noise commonly found in full text material. We use the method to create a protein name dictionary from a set of 80,528 full text articles. Only 8.3% of the names in this dictionary match SwissProt description lines. We assess the quality of the dictionary by studying its protein name recognition performance in full text. Conclusion This dictionary term lookup method compares favourably to other published methods, supporting the significance of our direct extraction approach. The method is strong in recognizing name variants not found in SwissProt. PMID:15817129

Risk disclosure and the recruitment of oocyte donors: are advertisers telling the full story?

PubMed

Alberta, Hillary B; Berry, Roberta M; Levine, Aaron D

2014-01-01

This study analyzes 435 oocyte donor recruitment advertisements to assess whether entities recruiting donors of oocytes to be used for in vitro fertilization (IVF) procedures include a disclosure of risks associated with the donation process in their advertisements. Such disclosure is required by the self-regulatory guidelines of the American Society for Reproductive Medicine (ASRM) and by law in California for advertisements placed in the state. We find very low rates of risk disclosure across entity types and regulatory regimes, although risk disclosure is more common in advertisements placed by entities subject to ASRM's self-regulatory guidelines. Advertisements placed in California are more likely to include risk disclosure, but disclosure rates are still quite low. California-based entities advertising outside the state are more likely to include risk disclosure than non-California entities, suggesting that California's law may have a modest "halo effect." Our results suggest that there is a significant ethical and policy problem with the status quo in light of the known and unknown risks of oocyte donation and the importance of risk disclosure to informed consent in the context of oocyte donation. © 2014 American Society of Law, Medicine & Ethics, Inc.

Towards an Obesity-Cancer Knowledge Base: Biomedical Entity Identification and Relation Detection

PubMed Central

Lossio-Ventura, Juan Antonio; Hogan, William; Modave, François; Hicks, Amanda; Hanna, Josh; Guo, Yi; He, Zhe; Bian, Jiang

2017-01-01

Obesity is associated with increased risks of various types of cancer, as well as a wide range of other chronic diseases. On the other hand, access to health information activates patient participation, and improve their health outcomes. However, existing online information on obesity and its relationship to cancer is heterogeneous ranging from pre-clinical models and case studies to mere hypothesis-based scientific arguments. A formal knowledge representation (i.e., a semantic knowledge base) would help better organizing and delivering quality health information related to obesity and cancer that consumers need. Nevertheless, current ontologies describing obesity, cancer and related entities are not designed to guide automatic knowledge base construction from heterogeneous information sources. Thus, in this paper, we present methods for named-entity recognition (NER) to extract biomedical entities from scholarly articles and for detecting if two biomedical entities are related, with the long term goal of building a obesity-cancer knowledge base. We leverage both linguistic and statistical approaches in the NER task, which supersedes the state-of-the-art results. Further, based on statistical features extracted from the sentences, our method for relation detection obtains an accuracy of 99.3% and a f-measure of 0.993. PMID:28503356

AN OVERVIEW OF COMPUTATIONAL LIFE SCIENCE DATABASES & EXCHANGE FORMATS OF RELEVANCE TO CHEMICAL BIOLOGY RESEARCH

PubMed Central

Hall, Aaron Smalter; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

2016-01-01

Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities. PMID:22934944

An overview of computational life science databases & exchange formats of relevance to chemical biology research.

PubMed

Smalter Hall, Aaron; Shan, Yunfeng; Lushington, Gerald; Visvanathan, Mahesh

2013-03-01

Databases and exchange formats describing biological entities such as chemicals and proteins, along with their relationships, are a critical component of research in life sciences disciplines, including chemical biology wherein small information about small molecule properties converges with cellular and molecular biology. Databases for storing biological entities are growing not only in size, but also in type, with many similarities between them and often subtle differences. The data formats available to describe and exchange these entities are numerous as well. In general, each format is optimized for a particular purpose or database, and hence some understanding of these formats is required when choosing one for research purposes. This paper reviews a selection of different databases and data formats with the goal of summarizing their purposes, features, and limitations. Databases are reviewed under the categories of 1) protein interactions, 2) metabolic pathways, 3) chemical interactions, and 4) drug discovery. Representation formats will be discussed according to those describing chemical structures, and those describing genomic/proteomic entities.

Religious Congregations’ HIV and Other Health Collaborations: With Whom Do They Work And What Do They Share?

PubMed Central

Werber, Laura; Derose, Kathryn Pitkin; Dominguez, Blanca X.; Mata, Michael A.

2012-01-01

This study explores how religious congregations interact with other community organizations to address health and, in particular, HIV-related needs within their membership and/or local communities. Case study data from a diverse sample of 14 urban congregations (6 African American, 4 Latino, 2 Anglo and 2 mixed race-ethnicity) indicate they engaged in three types of relationships to conduct HIV and other health-related activities, i.e. those where: 1) resources flowed to congregations from external entities; 2) resources flowed from congregations to external entities; 3) congregations interacted with external entities. These types of relationships were present in roughly equal proportions; thus, congregations were not primarily the recipients of resources from other organizations in these interactions. Financial, material, and human capital resources were shared across these three relationship types, and the most common organization types that congregations were involved with for health efforts were prevention and social service organizations, health care providers, and other congregations. In addition, congregations tended to have more collaborative relationships with other FBOs and to engage with non-FBOs more to either receive or provide resources. Results suggest that congregations contribute to community health by not only sponsoring health activities for their own members but also by providing specific support or resources to enhance the programming of other community organizations and collaborating with external organizations to sponsor congregation-based and community-based health activities. PMID:22491006

Developing a model for the adequate description of electronic communication in hospitals.

PubMed

Saboor, Samrend; Ammenwerth, Elske

2011-01-01

Adequate information and communication systems (ICT) can help to improve the communication in hospitals. Changes to the ICT-infrastructure of hospitals must be planed carefully. In order to support a comprehensive planning, we presented a classification of 81 common errors of the electronic communication on the MIE 2008 congress. Our objective now was to develop a data model that defines specific requirements for an adequate description of electronic communication processes We first applied the method of explicating qualitative content analysis on the error categorization in order to determine the essential process details. After this, we applied the method of subsuming qualitative content analysis on the results of the first step. A data model for the adequate description of electronic communication. This model comprises 61 entities and 91 relationships. The data model comprises and organizes all details that are necessary for the detection of the respective errors. It can be for either used to extend the capabilities of existing modeling methods or as a basis for the development of a new approach.

At 50 years of the description of acute respiratory distress syndrome.

PubMed

Carrillo-Esper, Raúl; Vázquez-De Anda, Gilberto Felipe; Mejía-Pérez, Cynthia Ivonne; Delaye-Aguilar, María Guadalupe; Pérez-Castañeda, Ana Ivonne; Briones-Garduño, Jesús Carlos; León-Ponce, Manuel Antonio Díaz de

2018-01-01

In 1967, Ashbaugh et al. published in the Lancet the description of a new entity, for which they coined the name "adult respiratory distress syndrome". On that article, they thoroughly described 12 patients who had respiratory distress with bilateral pulmonary infiltrates and oxygen therapy-refractory hypoxemia. For its management, emphasis was made on the importance of intubation and mechanical ventilation with positive end-expiratory pressure. At 50 years of its first publication, great advances on the knowledge of this condition have been achieved, which has influenced on patient management and survival. To celebrate this 50th anniversary, the National Academy of Medicine of Mexico organized a symposium with the purpose to spread the knowledge about this condition, recognize the researchers who made the original description and those who over the course of 50 years of history have contributed to its better understanding. The symposium addressed the topics of lung-kidney interaction, molecular bases of the disease and therapeutic advances. Copyright: © 2018 Secretaría de Salud.

History of Morgellons disease: the same name for different psychodermatologic diseases?

PubMed

Ferreira, Bárbara Roque; Roccia, Maria Grazia; Cardoso, José Carlos; França, Katlein; Wollina, Uwe; Lotti, Torello; Fioranelli, Massimo

2017-10-01

"Morgellons disease" has been a controversial topic in the history of psychodermatology. The most consensual scientific opinion is that it is a primary psychiatric disorder, particularly, a delusional disorder, although others were also pointed out. Some authors have suggested that it may correspond to a common dermatosis with secondary psychopathology. The Morgellons Research Foundation has advocated that it is "an emerging infectious" entity. This paper intends to critically review the main ideas and controversies, since its first description.

Inconspicuous Penis

PubMed Central

Srinivasan, Arun K.; Palmer, Lane S.; Palmer, Jeffrey S.

2011-01-01

Inconspicous penis refers to a constellation of conditions that make the penis look diminutive and small. This could be secondary to short penile shaft often termed as micropenis. But more commonly, this inconspicuous appearance is secondary to other causes ranging from congenital conditions such as penoscrotal webbing or megaprepuce, developmental conditions like prepubic adiposity that overhang the penis, and iatrogenic causes like trapped penis after adhesions secondary to circumcision. In this paper, we propose to define these entities and provide their descriptions and then to describe their management including surgical correction. PMID:22235186

Fractography of glass at the nanometer scale

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

Guilloteau, E.; Arribart, H.; Creuzet, F.

1996-12-01

The authors present a nanometer scale description of the fracture surface of soda-lime glass. This is achieved by the use of Atomic Force Microscopy. The mirror zone is shown to be built with elementary entities, the density of which increases continuously while the mist and hackle zones are approached. Moreover, the overall picture leads to some kind of self-similarity, in the sense that small regions of the hackle zone exhibit the full set of mirror, mist and hackle areas.

Research in DRM architecture based on watermarking and PKI

NASA Astrophysics Data System (ADS)

Liu, Ligang; Chen, Xiaosu; Xiao, Dao-ju; Yi, Miao

2005-02-01

Analyze the virtue and disadvantage of the present digital copyright protecting system, design a kind of security protocol model of digital copyright protection, which equilibrium consider the digital media"s use validity, integrality, security of transmission, and trade equity, make a detailed formalize description to the protocol model, analyze the relationship of the entities involved in the digital work copyright protection. The analysis of the security and capability of the protocol model shows that the model is good at security and practicability.

Collective learning modeling based on the kinetic theory of active particles

NASA Astrophysics Data System (ADS)

Burini, D.; De Lillo, S.; Gibelli, L.

2016-03-01

This paper proposes a systems approach to the theory of perception and learning in populations composed of many living entities. Starting from a phenomenological description of these processes, a mathematical structure is derived which is deemed to incorporate their complexity features. The modeling is based on a generalization of kinetic theory methods where interactions are described by theoretical tools of game theory. As an application, the proposed approach is used to model the learning processes that take place in a classroom.

Noun and knowledge retrieval for biological and non-biological entities following right occipitotemporal lesions.

PubMed

Bruffaerts, Rose; De Weer, An-Sofie; De Grauwe, Sophie; Thys, Miek; Dries, Eva; Thijs, Vincent; Sunaert, Stefan; Vandenbulcke, Mathieu; De Deyne, Simon; Storms, Gerrit; Vandenberghe, Rik

2014-09-01

We investigated the critical contribution of right ventral occipitotemporal cortex to knowledge of visual and functional-associative attributes of biological and non-biological entities and how this relates to category-specificity during confrontation naming. In a consecutive series of 7 patients with lesions confined to right ventral occipitotemporal cortex, we conducted an extensive assessment of oral generation of visual-sensory and functional-associative features in response to the names of biological and nonbiological entities. Subjects also performed a confrontation naming task for these categories. Our main novel finding related to a unique case with a small lesion confined to right medial fusiform gyrus who showed disproportionate naming impairment for nonbiological versus biological entities, specifically for tools. Generation of visual and functional-associative features was preserved for biological and non-biological entities. In two other cases, who had a relatively small posterior lesion restricted to primary visual and posterior fusiform cortex, retrieval of visual attributes was disproportionately impaired compared to functional-associative attributes, in particular for biological entities. However, these cases did not show a category-specific naming deficit. Two final cases with the largest lesions showed a classical dissociation between biological versus nonbiological entities during naming, with normal feature generation performance. This is the first lesion-based evidence of a critical contribution of the right medial fusiform cortex to tool naming. Second, dissociations along the dimension of attribute type during feature generation do not co-occur with category-specificity during naming in the current patient sample. Copyright © 2014 Elsevier Ltd. All rights reserved.

An enhanced digital line graph design

USGS Publications Warehouse

Guptill, Stephen C.

1990-01-01

In response to increasing information demands on its digital cartographic data, the U.S. Geological Survey has designed an enhanced version of the Digital Line Graph, termed Digital Line Graph - Enhanced (DLG-E). In the DLG-E model, the phenomena represented by geographic and cartographic data are termed entities. Entities represent individual phenomena in the real world. A feature is an abstraction of a set of entities, with the feature description encompassing only selected properties of the entities (typically the properties that have been portrayed cartographically on a map). Buildings, bridges, roads, streams, grasslands, and counties are examples of features. A feature instance, that is, one occurrence of a feature, is described in the digital environment by feature objects and spatial objects. A feature object identifies a feature instance and its nonlocational attributes. Nontopological relationships are associated with feature objects. The locational aspects of the feature instance are represented by spatial objects. Four spatial objects (points, nodes, chains, and polygons) and their topological relationships are defined. To link the locational and nonlocational aspects of the feature instance, a given feature object is associated with (or is composed of) a set of spatial objects. These objects, attributes, and relationships are the components of the DLG-E data model. To establish a domain of features for DLG-E, an approach using a set of classes, or views, of spatial entities was adopted. The five views that were developed are cover, division, ecosystem, geoposition, and morphology. The views are exclusive; each view is a self-contained analytical approach to the entire range of world features. Because each view is independent of the others, a single point on the surface of the Earth can be represented under multiple views. Under the five views, over 200 features were identified and defined. This set constitutes an initial domain of DLG-E features.

Network diffusion-based analysis of high-throughput data for the detection of differentially enriched modules

PubMed Central

Bersanelli, Matteo; Mosca, Ettore; Remondini, Daniel; Castellani, Gastone; Milanesi, Luciano

2016-01-01

A relation exists between network proximity of molecular entities in interaction networks, functional similarity and association with diseases. The identification of network regions associated with biological functions and pathologies is a major goal in systems biology. We describe a network diffusion-based pipeline for the interpretation of different types of omics in the context of molecular interaction networks. We introduce the network smoothing index, a network-based quantity that allows to jointly quantify the amount of omics information in genes and in their network neighbourhood, using network diffusion to define network proximity. The approach is applicable to both descriptive and inferential statistics calculated on omics data. We also show that network resampling, applied to gene lists ranked by quantities derived from the network smoothing index, indicates the presence of significantly connected genes. As a proof of principle, we identified gene modules enriched in somatic mutations and transcriptional variations observed in samples of prostate adenocarcinoma (PRAD). In line with the local hypothesis, network smoothing index and network resampling underlined the existence of a connected component of genes harbouring molecular alterations in PRAD. PMID:27731320

Convergent evolution of germ granule nucleators: A hypothesis.

PubMed

Kulkarni, Arpita; Extavour, Cassandra G

2017-10-01

Germ cells have been considered "the ultimate stem cell" because they alone, during normal development of sexually reproducing organisms, are able to give rise to all organismal cell types. Morphological descriptions of a specialized cytoplasm termed 'germ plasm' and associated electron dense ribonucleoprotein (RNP) structures called 'germ granules' within germ cells date back as early as the 1800s. Both germ plasm and germ granules are implicated in germ line specification across metazoans. However, at a molecular level, little is currently understood about the molecular mechanisms that assemble these entities in germ cells. The discovery that in some animals, the gene products of a small number of lineage-specific genes initiate the assembly (also termed nucleation) of germ granules and/or germ plasm is the first step towards facilitating a better understanding of these complex biological processes. Here, we draw on research spanning over 100years that supports the hypothesis that these nucleator genes may have evolved convergently, allowing them to perform analogous roles across animal lineages. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Stress fractures: pathophysiology, clinical presentation, imaging features, and treatment options.

PubMed

Matcuk, George R; Mahanty, Scott R; Skalski, Matthew R; Patel, Dakshesh B; White, Eric A; Gottsegen, Christopher J

2016-08-01

Stress fracture, in its most inclusive description, includes both fatigue and insufficiency fracture. Fatigue fractures, sometimes equated with the term "stress fractures," are most common in runners and other athletes and typically occur in the lower extremities. These fractures are the result of abnormal, cyclical loading on normal bone leading to local cortical resorption and fracture. Insufficiency fractures are common in elderly populations, secondary to osteoporosis, and are typically located in and around the pelvis. They are a result of normal or traumatic loading on abnormal bone. Subchondral insufficiency fractures of the hip or knee may cause acute pain that may present in the emergency setting. Medial tibial stress syndrome is a type of stress injury of the tibia related to activity and is a clinical syndrome encompassing a range of injuries from stress edema to frank-displaced fracture. Atypical subtrochanteric femoral fracture associated with long-term bisphosphonate therapy is also a recently discovered entity that needs early recognition to prevent progression to a complete fracture. Imaging recommendations for evaluation of stress fractures include initial plain radiographs followed, if necessary, by magnetic resonance imaging (MRI), which is preferred over computed tomography (CT) and bone scintigraphy. Radiographs are the first-line modality and may reveal linear sclerosis and periosteal reaction prior to the development of a frank fracture. MRI is highly sensitive with findings ranging from periosteal edema to bone marrow and intracortical signal abnormality. Additionally, a brief description of relevant clinical management of stress fractures is included.

Exposing the cancer genome atlas as a SPARQL endpoint

PubMed Central

Deus, Helena F.; Veiga, Diogo F.; Freire, Pablo R.; Weinstein, John N.; Mills, Gordon B.; Almeida, Jonas S.

2011-01-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. PMID:20851208

Hydrophilic Polymer-associated Ischemic Enterocolitis.

PubMed

Chavez, Jesus A; Chen, Wei; Frankel, Wendy L; Arnold, Christina A

2017-02-01

Hydrophilic polymer coating of medical devices serves to lubricate the device and prevent device-related complications. The coating can be mechanically disrupted and result in downstream injury via presumed thromboembolism. This process has been reported in the brain, heart, lung, and skin, and has been replicated through animal studies and in vitro histologic processing of the polymer coating. We report the first description of hydrophilic polymer-associated ischemic enterocolitis in a series of 7 specimens (small bowel=2, colon=4, aortic thrombus=1) from 3 patients. We report a 4% incidence among all patients with an ischemic bowel resection between April 29, 2014 and August 8, 2016. All patients developed bowel ischemia within 1 day of aortic repair, and all bowel resection specimens showed polymers, mainly in the submucosal vessels in areas of extensive ischemia. The polymers appeared as basophilic, intravascular, serpiginous structures. In a patient who developed acute paralysis after the aortic repair, identical polymers were identified in the aortic thrombus and the ischemic bowel segment. We demonstrate that the polymers display an altered morphology over time and with various graft types, and that the degrading polymers are associated with a foreign body giant cell reaction. Special stains can aid in diagnosis, with the polymers turquoise on a colloidal iron stain, pink on von Kossa and mucicarmine stains, and pale blue on trichrome. Clinical follow-up was available up to 115 weeks: 1 patient died, and 2 are alive and well. In summary, we report a new diagnostic entity to be considered in the differential diagnosis of iatrogenic ischemic injuries in the gastrointestinal tract. Awareness of this entity is important to elucidate the cause of ischemia and to prevent misdiagnosis of the polymers and their associated giant cell reaction as a parasitic infection, granulomatous vasculitis, sarcoidosis, and idiopathic inflammatory bowel disease.

Complement Coercion: The Joint Effects of Type and Typicality.

PubMed

Zarcone, Alessandra; McRae, Ken; Lenci, Alessandro; Padó, Sebastian

2017-01-01

Complement coercion ( begin a book → reading ) involves a type clash between an event-selecting verb and an entity-denoting object, triggering a covert event ( reading ). Two main factors involved in complement coercion have been investigated: the semantic type of the object (event vs. entity), and the typicality of the covert event ( the author began a book → writing ). In previous research, reading times have been measured at the object. However, the influence of the typicality of the subject-object combination on processing an aspectual verb such as begin has not been studied. Using a self-paced reading study, we manipulated semantic type and subject-object typicality, exploiting German word order to measure reading times at the aspectual verb. These variables interacted at the target verb. We conclude that both type and typicality probabilistically guide expectations about upcoming input. These results are compatible with an expectation-based view of complement coercion and language comprehension more generally in which there is rapid interaction between what is typically viewed as linguistic knowledge, and what is typically viewed as domain general knowledge about how the world works.

Complement Coercion: The Joint Effects of Type and Typicality

PubMed Central

Zarcone, Alessandra; McRae, Ken; Lenci, Alessandro; Padó, Sebastian

2017-01-01

Complement coercion (begin a book →reading) involves a type clash between an event-selecting verb and an entity-denoting object, triggering a covert event (reading). Two main factors involved in complement coercion have been investigated: the semantic type of the object (event vs. entity), and the typicality of the covert event (the author began a book →writing). In previous research, reading times have been measured at the object. However, the influence of the typicality of the subject–object combination on processing an aspectual verb such as begin has not been studied. Using a self-paced reading study, we manipulated semantic type and subject–object typicality, exploiting German word order to measure reading times at the aspectual verb. These variables interacted at the target verb. We conclude that both type and typicality probabilistically guide expectations about upcoming input. These results are compatible with an expectation-based view of complement coercion and language comprehension more generally in which there is rapid interaction between what is typically viewed as linguistic knowledge, and what is typically viewed as domain general knowledge about how the world works. PMID:29225585

78 FR 31882 - Demurrage Liability

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-28

... that these types of notices are generally already provided, often electronically. A review of the 2011... conflict with the proposed rules, rail carriers would need to update their demurrage tariffs to conform to... the classes of small entities that will be subject to the requirement and the type of professional...

Rapid Training of Information Extraction with Local and Global Data Views

DTIC Science & Technology

2012-05-01

relation type extension system based on active learning a relation type extension system based on semi-supervised learning, and a crossdomain...bootstrapping system for domain adaptive named entity extraction. The active learning procedure adopts features extracted at the sentence level as the local

Using Workflows to Explore and Optimise Named Entity Recognition for Chemistry

PubMed Central

Kolluru, BalaKrishna; Hawizy, Lezan; Murray-Rust, Peter; Tsujii, Junichi; Ananiadou, Sophia

2011-01-01

Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain), OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM) and pattern recognition based classifiers). Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER) accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR. PMID:21633495

Using workflows to explore and optimise named entity recognition for chemistry.

PubMed

Kolluru, Balakrishna; Hawizy, Lezan; Murray-Rust, Peter; Tsujii, Junichi; Ananiadou, Sophia

2011-01-01

Chemistry text mining tools should be interoperable and adaptable regardless of system-level implementation, installation or even programming issues. We aim to abstract the functionality of these tools from the underlying implementation via reconfigurable workflows for automatically identifying chemical names. To achieve this, we refactored an established named entity recogniser (in the chemistry domain), OSCAR and studied the impact of each component on the net performance. We developed two reconfigurable workflows from OSCAR using an interoperable text mining framework, U-Compare. These workflows can be altered using the drag-&-drop mechanism of the graphical user interface of U-Compare. These workflows also provide a platform to study the relationship between text mining components such as tokenisation and named entity recognition (using maximum entropy Markov model (MEMM) and pattern recognition based classifiers). Results indicate that, for chemistry in particular, eliminating noise generated by tokenisation techniques lead to a slightly better performance than others, in terms of named entity recognition (NER) accuracy. Poor tokenisation translates into poorer input to the classifier components which in turn leads to an increase in Type I or Type II errors, thus, lowering the overall performance. On the Sciborg corpus, the workflow based system, which uses a new tokeniser whilst retaining the same MEMM component, increases the F-score from 82.35% to 84.44%. On the PubMed corpus, it recorded an F-score of 84.84% as against 84.23% by OSCAR.

47 CFR 52.15 - Central office code administration.

Code of Federal Regulations, 2010 CFR

2010-10-01

... forecast data to the NANPA. (ii) Reporting shall be by separate legal entity and must include company name, company headquarters address, Operating Company Number (OCN), parent company OCN, and the primary type of... headquarters address, OCN, parent company's OCN(s), and the primary type of business in which the numbering...

A Type 3 prophage of “Candidatus Liberibacter asiaticus” carrying a restriction-modification system

USDA-ARS?s Scientific Manuscript database

Prophages, the lysogenic form of bacterial phages, are important genetic entities of “Candidatus Liberibacter asiaticus” (CLas), a non-culturable alfa-proteobacterium associated with citrus Huanglongbing (HLB). Two different CLas prophages are currently known, SC1 (Type 1) that has a lytic cycle and...

42 CFR 421.300 - Basis, applicability, and scope.

Code of Federal Regulations, 2010 CFR

2010-10-01

... types of entities eligible to become Medicare integrity program contractors. (2) Identifies the program... organizational conflicts of interest. (5) Prescribes responsibilities. (6) Sets forth limitations on contractor...

International Conference on Harmonisation; Guidance on Q11 Development and Manufacture of Drug Substances; availability. Notice.

PubMed

2012-11-20

The Food and Drug Administration (FDA) is announcing the availability of a guidance entitled "Q11 Development and Manufacture of Drug Substances.'' The guidance was prepared under the auspices of the International Conference on Harmonisation of Technical Requirements for Registration of Pharmaceuticals for Human Use (ICH). The guidance describes approaches to developing and understanding the manufacturing process of a drug substance and provides guidance on what information should be provided in certain sections of the Common Technical Document (CTD). The guidance is intended to harmonize the scientific and technical principles relating to the description and justification of the development and manufacturing process of drug substances (both chemical entities and biotechnological/biological entities) to enable a consistent approach for providing and evaluating this information across the three regions. The discussion of principles in the guidance is intended to apply only to the manufacture of drug substance, not the manufacture of finished drug products.

Liver abscess in ancient Greek and Greco-Roman texts.

PubMed

Papavramidou, Niki; Samara, Anastasia; Christopoulou-Aletra, Helen

2014-01-01

This paper presents liver abscesses, as studied in the ancient Greek and Greco-Roman bibliography. Numerous references concerning this entity can be found in the writings of the Hippocratic doctors (5th cent. B.C.), Archigenes of Apamea (1st cent. A.D.), Galen (2nd cent. A.D.), Aretaeus of Cappadocia (2nd cent. A.D), Oribasius (4th cent. A.D.), Theophilus Protospatharius (7th cent. A.D.), and Paulus Nicaeensis (7th-10th cent. A.D.). In most cases the clinical manifestations, the prognosis and the method of treatment are presented. In all ancient writings we studied, the rupture of a liver abscess is also part of the main theme. In specific, the path that the fluid would follow after a rupture was considered to be a main prognostic factor, i.e. if the fluid "coursed into the stomach", the patient would definitely die. In this work, an attempt is also made to correlate the ancient descriptions to modern medical entities, such as amebic or pyogenic liver abscess.

Bietti's tapetoretinal degeneration with marginal corneal dystrophy crystalline retinopathy.

PubMed Central

Welch, R B

1977-01-01

In 1937 Bietti reported a tapetoretinal degeneration with associated corneal deposits at the limbus. The hallmark of the disease was the crystalline characteristics of the retinal spots as well as those at the corneal limbus. Bagolini and Ioli-Spade in 1968 presented a 30 year follow-up on Bietti's cases and presented six additional cases. The present report delas with this entity in Orientals, a Chinese woman and a Japanese man. Corneal and conjunctival biopsy from the female patient revelaed a lipid deposition in both fibroblasts and epithelium. The term "crystalline retinopathy" has been added to the description of this entity since it defines the most characteristic feature of the syndrome. Images FIGURE 7 A FIGURE 7 B FIGURE 1 A FIGURE 1 B FIGURE 1 C FIGURE 2 A FIGURE 2 B FIGURE 2 C FIGURE 3 FIGURE 4 A FIGURE 4 B FIGURE 5 FIGURE 6 A FIGURE 6 B FIGURE 6 C FIGURE 8 PMID:306693

Phenex: ontological annotation of phenotypic diversity.

PubMed

Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; Midford, Peter E; Westerfield, Monte; Vision, Todd J

2010-05-05

Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

A CSP-Based Agent Modeling Framework for the Cougaar Agent-Based Architecture

NASA Technical Reports Server (NTRS)

Gracanin, Denis; Singh, H. Lally; Eltoweissy, Mohamed; Hinchey, Michael G.; Bohner, Shawn A.

2005-01-01

Cognitive Agent Architecture (Cougaar) is a Java-based architecture for large-scale distributed agent-based applications. A Cougaar agent is an autonomous software entity with behaviors that represent a real-world entity (e.g., a business process). A Cougaar-based Model Driven Architecture approach, currently under development, uses a description of system's functionality (requirements) to automatically implement the system in Cougaar. The Communicating Sequential Processes (CSP) formalism is used for the formal validation of the generated system. Two main agent components, a blackboard and a plugin, are modeled as CSP processes. A set of channels represents communications between the blackboard and individual plugins. The blackboard is represented as a CSP process that communicates with every agent in the collection. The developed CSP-based Cougaar modeling framework provides a starting point for a more complete formal verification of the automatically generated Cougaar code. Currently it is used to verify the behavior of an individual agent in terms of CSP properties and to analyze the corresponding Cougaar society.

Question mark ears, temporo-mandibular joint malformation and hypotonia: auriculo-condylar syndrome or a distinct entity?

PubMed

Priolo, M; Lerone, M; Rosaia, L; Calcagno, E P; Sadeghi, A K; Ghezzi, F; Ravazzolo, R; Silengo, M

2000-10-01

We report a boy with prominent, peculiarly malformed ears, abnormality of the ramus of the mandible and hypotonia. An isolated peculiar bilateral ear deformity named 'question mark ear' has been delineated in plastic reconstruction surgery reviews [Cosman et al., 1970 Plast Reconstr Surg 46:454-457; Cosman (1984) Plast Reconstr Surg 73:572-576; Takato et al. (1989) Ann Plast Surg 22:69-73; Brodovsky (1997) Plast Reconstr Surg 100:1254-1257; Park (1998) Plast Reconstr Surg 101:1620-1623; Al-Quattan (1998) Plast Reconstr Surg 102:439-441] and a similar deformity of the ear and changes in the temporo-mandibular joint and condyle has been described by Jampol et al. [(1998) Am J Med Genet 75:449-452] and by Guion-Almeida et al. [(1999) Am J Med Genet 86:130-133]. The present case may be the third description of this malformation complex with additional clinical features characterized by hypotonia and mild developmental delay, or possibly a new distinct entity.

Data fusion in cyber security: first order entity extraction from common cyber data

NASA Astrophysics Data System (ADS)

Giacobe, Nicklaus A.

2012-06-01

The Joint Directors of Labs Data Fusion Process Model (JDL Model) provides a framework for how to handle sensor data to develop higher levels of inference in a complex environment. Beginning from a call to leverage data fusion techniques in intrusion detection, there have been a number of advances in the use of data fusion algorithms in this subdomain of cyber security. While it is tempting to jump directly to situation-level or threat-level refinement (levels 2 and 3) for more exciting inferences, a proper fusion process starts with lower levels of fusion in order to provide a basis for the higher fusion levels. The process begins with first order entity extraction, or the identification of important entities represented in the sensor data stream. Current cyber security operational tools and their associated data are explored for potential exploitation, identifying the first order entities that exist in the data and the properties of these entities that are described by the data. Cyber events that are represented in the data stream are added to the first order entities as their properties. This work explores typical cyber security data and the inferences that can be made at the lower fusion levels (0 and 1) with simple metrics. Depending on the types of events that are expected by the analyst, these relatively simple metrics can provide insight on their own, or could be used in fusion algorithms as a basis for higher levels of inference.

A Novel Approach towards Medical Entity Recognition in Chinese Clinical Text

PubMed Central

Yu, Jian

2017-01-01

Medical entity recognition, a basic task in the language processing of clinical data, has been extensively studied in analyzing admission notes in alphabetic languages such as English. However, much less work has been done on nonstructural texts that are written in Chinese, or in the setting of differentiation of Chinese drug names between traditional Chinese medicine and Western medicine. Here, we propose a novel cascade-type Chinese medication entity recognition approach that aims at integrating the sentence category classifier from a support vector machine and the conditional random field-based medication entity recognition. We hypothesized that this approach could avoid the side effects of abundant negative samples and improve the performance of the named entity recognition from admission notes written in Chinese. Therefore, we applied this approach to a test set of 324 Chinese-written admission notes with manual annotation by medical experts. Our data demonstrated that this approach had a score of 94.2% in precision, 92.8% in recall, and 93.5% in F-measure for the recognition of traditional Chinese medicine drug names and 91.2% in precision, 92.6% in recall, and 91.7% F-measure for the recognition of Western medicine drug names. The differences in F-measure were significant compared with those in the baseline systems. PMID:29065612

IGES transformer and NURBS in grid generation

NASA Technical Reports Server (NTRS)

Yu, Tzu-Yi; Soni, Bharat K.

1993-01-01

In the field of Grid Generation and the CAD/CAM, there are numerous geometry output formats which require the designer to spend a great deal of time manipulating geometrical entities in order to achieve a useful sculptured geometrical description for grid generation. Also in this process, there is a danger of losing fidelity of the geometry under consideration. This stresses the importance of a standard geometry definition for the communication link between varying CAD/CAM and grid system. The IGES (Initial Graphics Exchange Specification) file is a widely used communication between CAD/CAM and the analysis tools. The scientists at NASA Research Centers - including NASA Ames, NASA Langley, NASA Lewis, NASA Marshall - have recognized this importance and, therefore, in 1992 they formed the committee of the 'NASA-IGES' which is the subset of the standard IGES. This committee stresses the importance and encourages the CFD community to use the standard IGES file for the interface between the CAD/CAM and CFD analysis. Also, two of the IGES entities -- the NURBS Curve (Entity 126) and NURBS Surface (Entity 128) -- which have many useful geometric properties -- like the convex hull property, local control property and affine invariance, also widely utilized analytical geometries can be accurately represented using NURBS. This is important in today grid generation tools because of the emphasis of the interactive design. To satisfy the geometry transformation between the CAD/CAM system and Grid Generation field, the CAGI (Computer Aided Geometry Design) developed, which include the Geometry Transformation, Geometry Manipulation and Geometry Generation as well as the user interface. This paper will present the successful development IGES file transformer and application of NURBS definition in the grid generation.

An Algorithm for Integrated Subsystem Embodiment and System Synthesis

NASA Technical Reports Server (NTRS)

Lewis, Kemper

1997-01-01

Consider the statement,'A system has two coupled subsystems, one of which dominates the design process. Each subsystem consists of discrete and continuous variables, and is solved using sequential analysis and solution.' To address this type of statement in the design of complex systems, three steps are required, namely, the embodiment of the statement in terms of entities on a computer, the mathematical formulation of subsystem models, and the resulting solution and system synthesis. In complex system decomposition, the subsystems are not isolated, self-supporting entities. Information such as constraints, goals, and design variables may be shared between entities. But many times in engineering problems, full communication and cooperation does not exist, information is incomplete, or one subsystem may dominate the design. Additionally, these engineering problems give rise to mathematical models involving nonlinear functions of both discrete and continuous design variables. In this dissertation an algorithm is developed to handle these types of scenarios for the domain-independent integration of subsystem embodiment, coordination, and system synthesis using constructs from Decision-Based Design, Game Theory, and Multidisciplinary Design Optimization. Implementation of the concept in this dissertation involves testing of the hypotheses using example problems and a motivating case study involving the design of a subsonic passenger aircraft.

Named Entity Recognition in Chinese Clinical Text Using Deep Neural Network.

PubMed

Wu, Yonghui; Jiang, Min; Lei, Jianbo; Xu, Hua

2015-01-01

Rapid growth in electronic health records (EHRs) use has led to an unprecedented expansion of available clinical data in electronic formats. However, much of the important healthcare information is locked in the narrative documents. Therefore Natural Language Processing (NLP) technologies, e.g., Named Entity Recognition that identifies boundaries and types of entities, has been extensively studied to unlock important clinical information in free text. In this study, we investigated a novel deep learning method to recognize clinical entities in Chinese clinical documents using the minimal feature engineering approach. We developed a deep neural network (DNN) to generate word embeddings from a large unlabeled corpus through unsupervised learning and another DNN for the NER task. The experiment results showed that the DNN with word embeddings trained from the large unlabeled corpus outperformed the state-of-the-art CRF's model in the minimal feature engineering setting, achieving the highest F1-score of 0.9280. Further analysis showed that word embeddings derived through unsupervised learning from large unlabeled corpus remarkably improved the DNN with randomized embedding, denoting the usefulness of unsupervised feature learning.

Evaluation and Cross-Comparison of Lexical Entities of Biological Interest (LexEBI)

PubMed Central

Rebholz-Schuhmann, Dietrich; Kim, Jee-Hyub; Yan, Ying; Dixit, Abhishek; Friteyre, Caroline; Hoehndorf, Robert; Backofen, Rolf; Lewin, Ian

2013-01-01

Motivation Biomedical entities, their identifiers and names, are essential in the representation of biomedical facts and knowledge. In the same way, the complete set of biomedical and chemical terms, i.e. the biomedical “term space” (the “Lexeome”), forms a key resource to achieve the full integration of the scientific literature with biomedical data resources: any identified named entity can immediately be normalized to the correct database entry. This goal does not only require that we are aware of all existing terms, but would also profit from knowing all their senses and their semantic interpretation (ambiguities, nestedness). Result This study compiles a resource for lexical terms of biomedical interest in a standard format (called “LexEBI”), determines the overall number of terms, their reuse in different resources and the nestedness of terms. LexEBI comprises references for protein and gene entries and their term variants and chemical entities amongst other terms. In addition, disease terms have been identified from Medline and PubmedCentral and added to LexEBI. Our analysis demonstrates that the baseforms of terms from the different semantic types show only little polysemous use. Nonetheless, the term variants of protein and gene names (PGNs) frequently contain species mentions, which should have been avoided according to protein annotation guidelines. Furthermore, the protein and gene entities as well as the chemical entities, both do comprise enzymes leading to hierarchical polysemy, and a large portion of PGNs make reference to a chemical entity. Altogether, according to our analysis based on the Medline distribution, 401,869 unique PGNs in the documents contain a reference to 25,022 chemical entities, 3,125 disease terms or 1,576 species mentions. Conclusion LexEBI delivers the complete biomedical and chemical Lexeome in a standardized representation (http://www.ebi.ac.uk/Rebholz-srv/LexEBI/). The resource provides the disease terms as open source content, and fully interlinks terms across resources. PMID:24124474

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

PubMed Central

2013-01-01

Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

The emergence of overweight as a disease entity: measuring up normality.

PubMed

Jutel, Annemarie

2006-11-01

As Charles Rosenberg [(2002). The tyranny of diagnosis. The Milbank Quarterly, 80, 237-260] has recently written, clinical diagnosis contributes to imposing structure on cultural reality in a manner which is not unproblematic. A social power resides in the process of naming diseases-one, which legitimises concerns, explains reality, naturalises deviance and imposes status. But clinical entities are not static, as both the concerns of society, and the technological ability of practitioners change (what Rosenberg refers to as the "iatrogenesis of nosology"), so too do the range of labels available for identifying disease. In this paper, I argue that being "overweight," once predominantly an adjectival descriptor of corpulence, a physical sign or a symptom, and even, in some cultures, a sign of wealth and status, is undergoing the transformation to disease entity. I suggest that evidence of this is present in both the frequency and the way in which the term is being used by the media, the medical establishment and the laity. I argue that this change stems from the convergence of two particular phenomena. The first is the belief in the neutrality of quantification, and the objectivity that measurement brings to qualitative description. The second is the importance attributed to normative appearance in health. I discuss some of the implications of this evolution and its impact on health practices, including the exploitation of this purported disease state for commercial benefit.

77 FR 46304 - Rimsulfuron; Pesticide Tolerances

Federal Register 2010, 2011, 2012, 2013, 2014

2012-08-03

... types of entities not listed in this unit could also be affected. The North American Industrial... e-CFR site at http://ecfr.gpoaccess.gov/cgi/t/text/text-idx?&c=ecfr&tpl=/ecfrbrowse/Title40/40tab_02... petition submitted to the Agency. The Office of Management and Budget (OMB) has exempted these types of...

[Adenomyosis: update on a frequent but difficult diagnosis].

PubMed

Wéry, O; Thille, A; Gaspard, U; van den Brûle, F

2005-11-01

Adenomyosis is a frequent entity, with difficult diagnosis, often obtained by pathological analysis performed after hysterectomy. This condition can cause abnormal uterine bleeding and dysmenorrhea, frequent reasons for consultation and hysterectomy. The development of ultrasonographic and magnetic resonance imaging techniques allow preoperative diagnosis. They also permit the use of hysteroscopic techniques for conservative uterine surgery, and have brought diagnosis and management of this disease to the front of the scene. This article reviews the pathological description of the disease, its epidemiology, clinical presentations, useful and necessary explorations, etiopathogeny and available therapies.

NASIS data base management system - IBM 360/370 OS MVT implementation. 4: Program design specifications

NASA Technical Reports Server (NTRS)

1973-01-01

The design specifications for the programs and modules within the NASA Aerospace Safety Information System (NASIS) are presented. The purpose of the design specifications is to standardize the preparation of the specifications and to guide the program design. Each major functional module within the system is a separate entity for documentation purposes. The design specifications contain a description of, and specifications for, all detail processing which occurs in the module. Sub-modules, reference tables, and data sets which are common to several modules are documented separately.

[Nose surgical anatomy in six aesthetic subunits].

PubMed

Chaput, B; Lauwers, F; Lopez, R; Saboye, J; André, A; Grolleau, J-L; Chavoin, J-P

2013-04-01

The nose is a complex entity, combining aesthetic and functional roles. Descriptive anatomy is a fundamental science that it can be difficult to relate directly to our daily surgical activity. Reasoning in terms of aesthetic subunits to decide on his actions appeared to us so obvious. The aim of this paper is to resume the anatomical bases relevant to our daily practice in order to fully apprehend the restorative or cosmetic procedures. We discuss the limits of the systematization of these principles in nasal oncology. Copyright © 2012 Elsevier Masson SAS. All rights reserved.

Literary psychiatric observation and diagnosis through the ages: King Lear revisited.

PubMed

Truskinovsky, Alexander M

2002-03-01

Shakespeare's plays, and in particular King Lear, have been a favorite source of clinical observation and diagnosis for psychiatrists for the past two centuries. Most authors agree that the description of Lear's mental symptoms is remarkably consistent and close to life. This article summarizes previous attempts to diagnose the mental illness of King Lear, featuring, among others, such entities as mania, senile dementia, delirium, depression, and brief reactive psychosis, and offers a new diagnosis according to the modern diagnostic criteria, namely, bipolar I disorder, most recent episode manic, severe with psychotic features.

Association of external auditory canal atresia, vertical talus, and hypertelorism: confirmation of Rasmussen syndrome.

PubMed

Julia, Sophie; Pedespan, Jean Michel; Boudard, Philippe; Barbier, Richard; Gavilan-Cellie, Isabelle; Chateil, Jean François; Lacombe, Didier

2002-06-15

In 1979, Rasmussen et al. reported six members of a family with congenital, bilateral, symmetrical, and isolated subtotal atresia of the external auditory canal, bilateral foot abnormalities, and increased interocular distance. The family history suggested autosomal dominant inheritance of the syndrome. We report a 3-year-old girl whose symptoms are compatible with this diagnosis. Therefore, we suggest confirmation of the description by Rasmussen et al. as a distinct entity and suggest the term Rasmussen syndrome for this condition. Copyright 2002 Wiley-Liss, Inc.

NASIS data base management system: IBM 360 TSS implementation. Volume 4: Program design specifications

NASA Technical Reports Server (NTRS)

1973-01-01

The design specifications for the programs and modules within the NASA Aerospace Safety Information System (NASIS) are presented. The purpose of the design specifications is to standardize the preparation of the specifications and to guide the program design. Each major functional module within the system is a separate entity for documentation purposes. The design specifications contain a description of, and specifications for, all detail processing which occurs in the module. Sub-models, reference tables, and data sets which are common to several modules are documented separately.

Necrotizing Infundibular Crystalline Folliculitis (NICF) Induced by Anti-Tumoral Therapies: Report of 2 Cases.

PubMed

Fattouh, Kinda; Collet-Benzaquen, Diane; Provensal, Anne M; Desseigne, Françoise; Castillo, Christine; Combemale, Patrick; de la Fouchardière, Arnaud

2017-10-01

Necrotizing Infundibular Crystalline Folliculitis (NICF) is rare entity of unknown pathogenesis presenting as follicular crystalline papules arising in seborrheic areas. We report 2 cases of NICF in patients under targeted therapy for metastatic adenocarcinoma. In one case, the lesions reappeared cyclically every 3 weeks after each injection and in the other case, lesions persisted until disruption of the continuous oral therapy. Punch-biopsies demonstrated folliculitis with a plugging crystalline material associated with either bacteria or yeast. These are the first descriptions of drug-induced NICF.

Collective learning modeling based on the kinetic theory of active particles.

PubMed

Burini, D; De Lillo, S; Gibelli, L

2016-03-01

This paper proposes a systems approach to the theory of perception and learning in populations composed of many living entities. Starting from a phenomenological description of these processes, a mathematical structure is derived which is deemed to incorporate their complexity features. The modeling is based on a generalization of kinetic theory methods where interactions are described by theoretical tools of game theory. As an application, the proposed approach is used to model the learning processes that take place in a classroom. Copyright © 2015 Elsevier B.V. All rights reserved.

Naming unique entities in the semantic variant of primary progressive aphasia and Alzheimer's disease: Towards a better understanding of the semantic impairment.

PubMed

Montembeault, M; Brambati, S M; Joubert, S; Boukadi, M; Chapleau, M; Laforce, R Jr; Wilson, M A; Macoir, J; Rouleau, I

2017-01-27

While the semantic variant of primary progressive aphasia (svPPA) is characterized by a predominant semantic memory impairment, episodic memory impairments are the clinical hallmark of Alzheimer's disease (AD). However, AD patients also present with semantic deficits, which are more severe for semantically unique entities (e.g. a famous person) than for common concepts (e.g. a beaver). Previous studies in these patient populations have largely focused on famous-person naming. Therefore, we aimed to evaluate if these impairments also extend to other semantically unique entities such as famous places and famous logos. In this study, 13 AD patients, 9 svPPA patients, and 12 cognitively unimpaired elderly subjects (CTRL) were tested with a picture-naming test of non-unique entities (Boston Naming Test) and three experimental tests of semantically unique entities assessing naming of famous persons, places, and logos. Both clinical groups were overall more impaired at naming semantically unique entities than non-unique entities. Naming impairments in AD and svPPA extended to the other types of semantically unique entities, since a CTRL>AD>svPPA pattern was found on the performance of all naming tests. Naming famous places and famous persons appeared to be most impaired in svPPA, and both specific and general semantic knowledge for these entities were affected in these patients. Although AD patients were most significantly impaired on famous-person naming, only their specific semantic knowledge was impaired, while general knowledge was preserved. Post-hoc neuroimaging analyses also showed that famous-person naming impairments in AD correlated with atrophy in the temporo-parietal junction, a region functionally associated with lexical access. In line with previous studies, svPPA patients' impairment in both naming and semantic knowledge suggest a more profound semantic impairment, while naming impairments in AD may arise to a greater extent from impaired lexical access, even though semantic impairment for specific knowledge is also present. These results highlight the critical importance of developing and using a variety of semantically-unique-entity naming tests in neuropsychological assessments of patients with neurodegenerative diseases, which may unveil different patterns of lexical-semantic deficits. Copyright © 2016 Elsevier Ltd. All rights reserved.

[Sublethal microcephalic chondrodysplasia. Taybi-Linder syndrome, primordial microcephalic nanism types I and III].

PubMed

Maroteaux, P; Badoual, J

1990-02-01

The authors describe a case of microcephalic dwarfism observed in a newborn until 10 months of age and discuss the diagnostic challenge. They show that the Taybi-Linder syndrome and the primordial dwarfism type I and type III of Majewski are an identical recessive autosomal entity. The radiological evolution explains the initial separation of type I and type III. Because of the skeletal lesions, lacking in the Seckel syndrome, the name of sublethal microcephalic chondrodysplasia is proposed for this disease.

77 FR 37025 - Final Priority: Disability Rehabilitation Research Project-Burn Model Systems Centers

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-20

... other types of research, including but not limited to, descriptive research, exploratory research, and... interventions research and descriptive research, exploratory research, measures development, or other types of... injury or to conduct other types of research, including but not limited to, descriptive research...

78 FR 7765 - Information Collection; Submission for OMB Review, Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2013-02-04

... certifying entities to verify, certify and order the President's Volunteer Service Awards. Type of Review... minutes. Estimated Total Burden Hours: 66,666. Total Burden Cost (capital/startup): None. Total Burden...

75SeHCAT scan in bile acid malabsorption in chronic diarrhoea.

PubMed

Mena Bares, L M; Carmona Asenjo, E; García Sánchez, M V; Moreno Ortega, E; Maza Muret, F R; Guiote Moreno, M V; Santos Bueno, A M; Iglesias Flores, E; Benítez Cantero, J M; Vallejo Casas, J A

Chronic diarrhoea is a common entity in daily clinical practice and it leads to a loss in these patients quality of life. It may be the main symptom of multiple ethiologies including bile acid malabsorption (BAM) which has a comparable prevalence to celiac disease. The BAM results from imbalances in the homeostasis of bile acids in the enterohepatic circulation. It can be a consequence of ileal disease or ileal dysfunction (BAM type i), it can be considered idiopathic or primary (BAM type ii) or associated with other gastrointestinal entities (BAM type iii). Among the different diagnostic methods available, 75 SeHCAT study is the primary current method due to its sensitivity, specificity, safety and low cost. The main disadvantage is that it's not available in all countries, so other diagnostic methods have appeared, such as serum measurement of FGF19 and C4, however they are significantly more complex and costly. The first-line treatment of bile acid diarrhoea is bile acid sequestrant, such as cholestyramine, which can be difficult to administer due to its poor tolerability and gastrointestinal side effects. These are less prominent with newer agents such as colesevelam. In summary, the BAM is a common entity underdiagnosed and undertreated, so it is essential to establish a diagnosis algorithm of chronic diarrhoea in which the 75 SeHCAT study would be first or second line in the differential diagnosis of these patients. Copyright © 2016 Elsevier España, S.L.U. y SEMNIM. All rights reserved.

Muscle pain in the head: overlap between temporomandibular disorders and tension-type headaches.

PubMed

Svensson, Peter

2007-06-01

A variety of painful problems can affect the muscles in the head and face. Both temporomandibular disorders and tension-type headaches are believed to have a significant contribution from the skeletal muscles and have several clinical features in common. It still unclear, however, to what extent these two prevalent disorders are separate entities or have similar pathophysiological background. There is now reasonably good evidence that myofascial temporomandibular disorder patients are more likely to have a tension-type headache problem and vice versa, but the overlap is not complete. Studies have documented similarities regarding sensitization of the nociceptive pathways, dysfunction of the endogenous pain modulatory systems as well as contributing genetic factors, but there are also a number of distinct differences between temporomandibular disorders and tension-type headaches that need to be considered. Using the current classification systems, myofascial temporomandibular disorder pain and tension-type headache disorders do overlap and appear to share many of the same pathophysiological mechanisms, but it would be premature to consider them as identical entities since the importance of, for example, the affected muscles and associated function and genetic background needs to be established. Orofacial pain and headache specialists should collaborate to further develop diagnostic procedures and management strategies of temporomandibular disorders and tension-type headaches.

Exposing the cancer genome atlas as a SPARQL endpoint.

PubMed

Deus, Helena F; Veiga, Diogo F; Freire, Pablo R; Weinstein, John N; Mills, Gordon B; Almeida, Jonas S

2010-12-01

The Cancer Genome Atlas (TCGA) is a multidisciplinary, multi-institutional effort to characterize several types of cancer. Datasets from biomedical domains such as TCGA present a particularly challenging task for those interested in dynamically aggregating its results because the data sources are typically both heterogeneous and distributed. The Linked Data best practices offer a solution to integrate and discover data with those characteristics, namely through exposure of data as Web services supporting SPARQL, the Resource Description Framework query language. Most SPARQL endpoints, however, cannot easily be queried by data experts. Furthermore, exposing experimental data as SPARQL endpoints remains a challenging task because, in most cases, data must first be converted to Resource Description Framework triples. In line with those requirements, we have developed an infrastructure to expose clinical, demographic and molecular data elements generated by TCGA as a SPARQL endpoint by assigning elements to entities of the Simple Sloppy Semantic Database (S3DB) management model. All components of the infrastructure are available as independent Representational State Transfer (REST) Web services to encourage reusability, and a simple interface was developed to automatically assemble SPARQL queries by navigating a representation of the TCGA domain. A key feature of the proposed solution that greatly facilitates assembly of SPARQL queries is the distinction between the TCGA domain descriptors and data elements. Furthermore, the use of the S3DB management model as a mediator enables queries to both public and protected data without the need for prior submission to a single data source. Copyright © 2010 Elsevier Inc. All rights reserved.

Imposing a Lagrangian Particle Framework on an Eulerian Hydrodynamics Infrastructure in Flash

NASA Technical Reports Server (NTRS)

Dubey, A.; Daley, C.; ZuHone, J.; Ricker, P. M.; Weide, K.; Graziani, C.

2012-01-01

In many astrophysical simulations, both Eulerian and Lagrangian quantities are of interest. For example, in a galaxy cluster merger simulation, the intracluster gas can have Eulerian discretization, while dark matter can be modeled using particles. FLASH, a component-based scientific simulation code, superimposes a Lagrangian framework atop an adaptive mesh refinement Eulerian framework to enable such simulations. The discretization of the field variables is Eulerian, while the Lagrangian entities occur in many different forms including tracer particles, massive particles, charged particles in particle-in-cell mode, and Lagrangian markers to model fluid structure interactions. These widely varying roles for Lagrangian entities are possible because of the highly modular, flexible, and extensible architecture of the Lagrangian framework. In this paper, we describe the Lagrangian framework in FLASH in the context of two very different applications, Type Ia supernovae and galaxy cluster mergers, which use the Lagrangian entities in fundamentally different ways.

Imposing a Lagrangian Particle Framework on an Eulerian Hydrodynamics Infrastructure in FLASH

NASA Astrophysics Data System (ADS)

Dubey, A.; Daley, C.; ZuHone, J.; Ricker, P. M.; Weide, K.; Graziani, C.

2012-08-01

In many astrophysical simulations, both Eulerian and Lagrangian quantities are of interest. For example, in a galaxy cluster merger simulation, the intracluster gas can have Eulerian discretization, while dark matter can be modeled using particles. FLASH, a component-based scientific simulation code, superimposes a Lagrangian framework atop an adaptive mesh refinement Eulerian framework to enable such simulations. The discretization of the field variables is Eulerian, while the Lagrangian entities occur in many different forms including tracer particles, massive particles, charged particles in particle-in-cell mode, and Lagrangian markers to model fluid-structure interactions. These widely varying roles for Lagrangian entities are possible because of the highly modular, flexible, and extensible architecture of the Lagrangian framework. In this paper, we describe the Lagrangian framework in FLASH in the context of two very different applications, Type Ia supernovae and galaxy cluster mergers, which use the Lagrangian entities in fundamentally different ways.

The formulation of argument structure in SLI: an eye-movement study

PubMed Central

ANDREU, LLORENÇ; SANZ-TORRENT, MÒNICA; OLMOS, JOAN GUÀRDIA; MACWHINNEY, BRIAN

2014-01-01

This study investigated the formulation of verb argument structure in Catalan- and Spanish-speaking children with specific language impairment (SLI) and typically developing age-matched controls. We compared how language production can be guided by conceptual factors, such as the organization of the entities participating in an event and knowledge regarding argument structure. Eleven children with SLI (aged 3;8 to 6;6) and eleven control children participated in an eye-tracking experiment in which participants had to describe events with different argument structure in the presence of visual scenes. Picture descriptions, latency time and eye movements were recorded and analyzed. The picture description results showed that the percentage of responses in which children with SLI substituted a non-target verb for the target verb was significantly different from that for the control group. Children with SLI made more omissions of obligatory arguments, especially of themes, as the verb argument complexity increased. Moreover, when the number of arguments of the verb increased, the children took more time to begin their descriptions, but no differences between groups were found. For verb type latency, all children were significantly faster to start describing one-argument events than two- and three-argument events. No differences in latency time were found between two- and three-argument events. There were no significant differences between the groups. Eye-movement showed that children with SLI looked less at the event zone than the age-matched controls during the first two seconds. These differences between the groups were significant for three-argument verbs, and only marginally significant for one- and two-argument verbs. Children with SLI also spent significantly less time looking at the theme zones than their age-matched controls. We suggest that both processing limitations and deficits in the semantic representation of verbs may play a role in these difficulties. PMID:23294226

The Effect of a Truly Liberal Education on Society.

ERIC Educational Resources Information Center

Earl, Archie W., Sr.

A liberal education (in which the student is exposed to a variety of different religions, political systems, economic systems, cultures, types of art work, and types of music) helps the student develop an appreciation of all these entities. In college, students are drawn from different states and school districts, and even different parts of the…

NOUS: A Knowledge Graph Management System

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

Knowledge graphs represent information as entities and relationships between them. For tasks such as natural language question answering or automated analysis of text, a knowledge graph provides valuable context to establish the specific type of entities being discussed. It allow us to derive better context about newly arriving information and leads to intelligent reasoning capabilities. We address two primary needs: A) Automated construction of knowledge graphs is a technically challenging, expensive process; and B) The ability to synthesize new information by monitoring newly emerging knowledge is a transformational capability that does not exist in state of the art systems.

Pectus excavatum: history, hypotheses and treatment options

PubMed Central

Brochhausen, Christoph; Turial, Salmai; Müller, Felix K.P.; Schmitt, Volker H.; Coerdt, Wiltrud; Wihlm, Jean-Marie; Schier, Felix; Kirkpatrick, C. James

2012-01-01

Pectus excavatum and pectus carinatum represent the most frequent chest wall deformations. However, the pathogenesis is still poorly understood and research results remain inconsistent. To focus on the recent state of knowledge, we summarize and critically discuss the pathological concepts based on the history of these entities, beginning with the first description in the sixteenth century. Based on the early clinical descriptions, we review and discuss the different pathogenetic hypotheses. To open new perspectives for the potential pathomechanisms, the embryonic and foetal development of the ribs and the sternum is highlighted following the understanding that the origin of these deformities is given by the disruption in the maturation of the parasternal region. In the second, different therapeutical techniques are highlighted and based on the pathogenetic hypotheses and the embryological knowledge potential new biomaterial-based perspectives with interesting insights for tissue engineering-based treatment options are presented. PMID:22394989

Risk transfer modeling among hierarchically associated stakeholders in development of space systems

NASA Astrophysics Data System (ADS)

Henkle, Thomas Grove, III

Research develops an empirically derived cardinal model that prescribes handling and transfer of risks between organizations with hierarchical relationships. Descriptions of mission risk events, risk attitudes, and conditions for risk transfer are determined for client and underwriting entities associated with acquisition, production, and deployment of space systems. The hypothesis anticipates that large client organizations should be able to assume larger dollar-value risks of a program in comparison to smaller organizations even though many current risk transfer arrangements via space insurance violate this hypothesis. A literature survey covers conventional and current risk assessment methods, current techniques used in the satellite industry for complex system development, cardinal risk modeling, and relevant aspects of utility theory. Data gathered from open literature on demonstrated launch vehicle and satellite in-orbit reliability, annual space insurance premiums and losses, and ground fatalities and range damage associated with satellite launch activities are presented. Empirically derived models are developed for risk attitudes of space system clients and third-party underwriters associated with satellite system development and deployment. Two application topics for risk transfer are examined: the client-underwriter relationship on assumption or transfer of risks associated with first-year mission success, and statutory risk transfer agreements between space insurance underwriters and the US government to promote growth in both commercial client and underwriting industries. Results indicate that client entities with wealth of at least an order of magnitude above satellite project costs should retain risks to first-year mission success despite present trends. Furthermore, large client entities such as the US government should never pursue risk transfer via insurance under previously demonstrated probabilities of mission success; potential savings may reasonably exceed multiple tens of $millions per space project. Additional results indicate that current US government statutory arrangements on risk sharing with underwriting entities appears reasonable with respect to stated objectives. This research combines aspects of multiple disciplines to include risk management, decision theory, utility theory, and systems architecting. It also demonstrates development of a more general theory on prescribing risk transfer criteria between distinct, but hierarchically associated entities involved in complex system development with applicability to a variety of technical domains.

C4ISR Architecture Working Group (AWG), Architecture Framework Version 2.0.

DTIC Science & Technology

1997-12-18

Vision Name Name/identifier of document that contains doctrine, goals, or vision Type Doctrine, goals, or vision Description Text summary description...e.g., organization, directive, order) Description Text summary of tasking •Rules, Criteria, or Conventions Name Name/identifier of document that...contains rules, criteria, or conventions Type One of: rules, criteria, or conventions Description Text summary description of contents or

Describing different brain computer interface systems through a unique model: a UML implementation.

PubMed

Quitadamo, Lucia Rita; Marciani, Maria Grazia; Cardarilli, Gian Carlo; Bianchi, Luigi

2008-01-01

All the protocols currently implemented in brain computer interface (BCI) experiments are characterized by different structural and temporal entities. Moreover, due to the lack of a unique descriptive model for BCI systems, there is not a standard way to define the structure and the timing of a BCI experimental session among different research groups and there is also great discordance on the meaning of the most common terms dealing with BCI, such as trial, run and session. The aim of this paper is to provide a unified modeling language (UML) implementation of BCI systems through a unique dynamic model which is able to describe the main protocols defined in the literature (P300, mu-rhythms, SCP, SSVEP, fMRI) and demonstrates to be reasonable and adjustable according to different requirements. This model includes a set of definitions of the typical entities encountered in a BCI, diagrams which explain the structural correlations among them and a detailed description of the timing of a trial. This last represents an innovation with respect to the models already proposed in the literature. The UML documentation and the possibility of adapting this model to the different BCI systems built to date, make it a basis for the implementation of new systems and a mean for the unification and dissemination of resources. The model with all the diagrams and definitions reported in the paper are the core of the body language framework, a free set of routines and tools for the implementation, optimization and delivery of cross-platform BCI systems.

The impact of the Patient Self-Determination Act's requirement that states describe law concerning patients' rights.

PubMed

Teno, Joan M; Sabatino, Charles; Parisier, Lauren; Rouse, Fenella; Lynn, Joanne

1993-01-01

As of December 1991, the Patient Self-Determination Act (PSDA) mandated that health care institutions which receive funding from Medicare or Medicaid provide written information about persons' rights to participate in medical decision-making and formulate advance directives. The PSDA required each state "...acting through a State agency, association, or other private nonprofit entity develop a written description of the law of the State (whether statutory or as recognized by the courts of the State) concerning advance directives that would be distributed by providers or organizations under the requirements of [the Act]." This mandate allowed each state considerable flexibility in its approach to the process of writing the state description and to its content. In 1990, the American Bar Association's Commission on Legal Problems of the Elderly prepared and distributed the Patient Self Determination Act: State Law Guide to assist each state in preparing its written description of state law. In follow-up to the distribution of this guide, we conducted a telephone survey with a representative from each state (including the District of Columbia) about each state's process for writing the state law description. This paper presents an evaluation of the process used by the states and of the documents they produced.

Carbon-dioxide emissions trading and hierarchical structure in worldwide finance and commodities markets.

PubMed

Zheng, Zeyu; Yamasaki, Kazuko; Tenenbaum, Joel N; Stanley, H Eugene

2013-01-01

In a highly interdependent economic world, the nature of relationships between financial entities is becoming an increasingly important area of study. Recently, many studies have shown the usefulness of minimal spanning trees (MST) in extracting interactions between financial entities. Here, we propose a modified MST network whose metric distance is defined in terms of cross-correlation coefficient absolute values, enabling the connections between anticorrelated entities to manifest properly. We investigate 69 daily time series, comprising three types of financial assets: 28 stock market indicators, 21 currency futures, and 20 commodity futures. We show that though the resulting MST network evolves over time, the financial assets of similar type tend to have connections which are stable over time. In addition, we find a characteristic time lag between the volatility time series of the stock market indicators and those of the EU CO(2) emission allowance (EUA) and crude oil futures (WTI). This time lag is given by the peak of the cross-correlation function of the volatility time series EUA (or WTI) with that of the stock market indicators, and is markedly different (>20 days) from 0, showing that the volatility of stock market indicators today can predict the volatility of EU emissions allowances and of crude oil in the near future.

Carbon-dioxide emissions trading and hierarchical structure in worldwide finance and commodities markets

NASA Astrophysics Data System (ADS)

Zheng, Zeyu; Yamasaki, Kazuko; Tenenbaum, Joel N.; Stanley, H. Eugene

2013-01-01

In a highly interdependent economic world, the nature of relationships between financial entities is becoming an increasingly important area of study. Recently, many studies have shown the usefulness of minimal spanning trees (MST) in extracting interactions between financial entities. Here, we propose a modified MST network whose metric distance is defined in terms of cross-correlation coefficient absolute values, enabling the connections between anticorrelated entities to manifest properly. We investigate 69 daily time series, comprising three types of financial assets: 28 stock market indicators, 21 currency futures, and 20 commodity futures. We show that though the resulting MST network evolves over time, the financial assets of similar type tend to have connections which are stable over time. In addition, we find a characteristic time lag between the volatility time series of the stock market indicators and those of the EU CO2 emission allowance (EUA) and crude oil futures (WTI). This time lag is given by the peak of the cross-correlation function of the volatility time series EUA (or WTI) with that of the stock market indicators, and is markedly different (>20 days) from 0, showing that the volatility of stock market indicators today can predict the volatility of EU emissions allowances and of crude oil in the near future.

Computational Evolutionary Methodology for Knowledge Discovery and Forecasting in Epidemiology and Medicine

NASA Astrophysics Data System (ADS)

Rao, Dhananjai M.; Chernyakhovsky, Alexander; Rao, Victoria

2008-05-01

Humanity is facing an increasing number of highly virulent and communicable diseases such as avian influenza. Researchers believe that avian influenza has potential to evolve into one of the deadliest pandemics. Combating these diseases requires in-depth knowledge of their epidemiology. An effective methodology for discovering epidemiological knowledge is to utilize a descriptive, evolutionary, ecological model and use bio-simulations to study and analyze it. These types of bio-simulations fall under the category of computational evolutionary methods because the individual entities participating in the simulation are permitted to evolve in a natural manner by reacting to changes in the simulated ecosystem. This work describes the application of the aforementioned methodology to discover epidemiological knowledge about avian influenza using a novel eco-modeling and bio-simulation environment called SEARUMS. The mathematical principles underlying SEARUMS, its design, and the procedure for using SEARUMS are discussed. The bio-simulations and multi-faceted case studies conducted using SEARUMS elucidate its ability to pinpoint timelines, epicenters, and socio-economic impacts of avian influenza. This knowledge is invaluable for proactive deployment of countermeasures in order to minimize negative socioeconomic impacts, combat the disease, and avert a pandemic.

Computational Evolutionary Methodology for Knowledge Discovery and Forecasting in Epidemiology and Medicine

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

Rao, Dhananjai M.; Chernyakhovsky, Alexander; Rao, Victoria

2008-05-08

Humanity is facing an increasing number of highly virulent and communicable diseases such as avian influenza. Researchers believe that avian influenza has potential to evolve into one of the deadliest pandemics. Combating these diseases requires in-depth knowledge of their epidemiology. An effective methodology for discovering epidemiological knowledge is to utilize a descriptive, evolutionary, ecological model and use bio-simulations to study and analyze it. These types of bio-simulations fall under the category of computational evolutionary methods because the individual entities participating in the simulation are permitted to evolve in a natural manner by reacting to changes in the simulated ecosystem. Thismore » work describes the application of the aforementioned methodology to discover epidemiological knowledge about avian influenza using a novel eco-modeling and bio-simulation environment called SEARUMS. The mathematical principles underlying SEARUMS, its design, and the procedure for using SEARUMS are discussed. The bio-simulations and multi-faceted case studies conducted using SEARUMS elucidate its ability to pinpoint timelines, epicenters, and socio-economic impacts of avian influenza. This knowledge is invaluable for proactive deployment of countermeasures in order to minimize negative socioeconomic impacts, combat the disease, and avert a pandemic.« less

Intelligent Entity Behavior Within Synthetic Environments. Chapter 3

NASA Technical Reports Server (NTRS)

Kruk, R. V.; Howells, P. B.; Siksik, D. N.

2007-01-01

This paper describes some elements in the development of realistic performance and behavior in the synthetic entities (players) which support Modeling and Simulation (M&S) applications, particularly military training. Modern human-in-the-loop (virtual) training systems incorporate sophisticated synthetic environments, which provide: 1. The operational environment, including, for example, terrain databases; 2. Physical entity parameters which define performance in engineered systems, such as aircraft aerodynamics; 3. Platform/system characteristics such as acoustic, IR and radar signatures; 4. Behavioral entity parameters which define interactive performance, including knowledge/reasoning about terrain, tactics; and, 5. Doctrine, which combines knowledge and tactics into behavior rule sets. The resolution and fidelity of these model/database elements can vary substantially, but as synthetic environments are designed to be compose able, attributes may easily be added (e.g., adding a new radar to an aircraft) or enhanced (e.g. Amending or replacing missile seeker head/ Electronic Counter Measures (ECM) models to improve the realism of their interaction). To a human in the loop with synthetic entities, their observed veridicality is assessed via engagement responses (e.g. effect of countermeasures upon a closing missile), as seen on systems displays, and visual (image) behavior. The realism of visual models in a simulation (level of detail as well as motion fidelity) remains a challenge in realistic articulation of elements such as vehicle antennae and turrets, or, with human figures; posture, joint articulation, response to uneven ground. Currently the adequacy of visual representation is more dependant upon the quality and resolution of the physical models driving those entities than graphics processing power per Se. Synthetic entities in M&S applications traditionally have represented engineered systems (e.g. aircraft) with human-in-the-loop performance characteristics (e.g. visual acuity) included in the system behavioral specification. As well, performance affecting human parameters such as experience level, fatigue and stress are coming into wider use (via AI approaches) to incorporate more uncertainty as to response type as well as performance (e.g. Where an opposing entity might go and what it might do, as well as how well it might perform).

Clinical Documents: Attribute-Values Entity Representation, Context, Page Layout And Communication

PubMed Central

Lovis, Christian; Lamb, Alexander; Baud, Robert; Rassinoux, Anne-Marie; Fabry, Paul; Geissbühler, Antoine

2003-01-01

This paper presents how acquisition, storage and communication of clinical documents are implemented at the University Hospitals of Geneva. Careful attention has been given to user-interfaces, in order to support complex layouts, spell checking, templates management with automatic prefilling in order to facilitate acquisition. A dual architecture has been developed for storage using an attributes-values entity unified database and a consolidated, patient-centered, layout-respectful files-based storage, providing both representation power and sinsert (peed of accesses. This architecture allows great flexibility to store a continuum of data types from simple type values up to complex clinical reports. Finally, communication is entirely based on HTTP-XML internally and a HL-7 CDA interface V2 is currently studied for external communication. Some of the problem encountered, mostly concerning the typology of documents and the ontology of clinical attributes are evoked. PMID:14728202

A System for Modelling Cell–Cell Interactions during Plant Morphogenesis

PubMed Central

Dupuy, Lionel; Mackenzie, Jonathan; Rudge, Tim; Haseloff, Jim

2008-01-01

Background and aims During the development of multicellular organisms, cells are capable of interacting with each other through a range of biological and physical mechanisms. A description of these networks of cell–cell interactions is essential for an understanding of how cellular activity is co-ordinated in regionalized functional entities such as tissues or organs. The difficulty of experimenting on living tissues has been a major limitation to describing such systems, and computer modelling appears particularly helpful to characterize the behaviour of multicellular systems. The experimental difficulties inherent to the multitude of parallel interactions that underlie cellular morphogenesis have led to the need for computer models. Methods A new generic model of plant cellular morphogenesis is described that expresses interactions amongst cellular entities explicitly: the plant is described as a multi-scale structure, and interactions between distinct entities is established through a topological neighbourhood. Tissues are represented as 2D biphasic systems where the cell wall responds to turgor pressure through a viscous yielding of the cell wall. Key Results This principle was used in the development of the CellModeller software, a generic tool dedicated to the analysis and modelling of plant morphogenesis. The system was applied to three contrasting study cases illustrating genetic, hormonal and mechanical factors involved in plant morphogenesis. Conclusions Plant morphogenesis is fundamentally a cellular process and the CellModeller software, through its underlying generic model, provides an advanced research tool to analyse coupled physical and biological morphogenetic mechanisms. PMID:17921524

Extracting laboratory test information from biomedical text

PubMed Central

Kang, Yanna Shen; Kayaalp, Mehmet

2013-01-01

Background: No previous study reported the efficacy of current natural language processing (NLP) methods for extracting laboratory test information from narrative documents. This study investigates the pathology informatics question of how accurately such information can be extracted from text with the current tools and techniques, especially machine learning and symbolic NLP methods. The study data came from a text corpus maintained by the U.S. Food and Drug Administration, containing a rich set of information on laboratory tests and test devices. Methods: The authors developed a symbolic information extraction (SIE) system to extract device and test specific information about four types of laboratory test entities: Specimens, analytes, units of measures and detection limits. They compared the performance of SIE and three prominent machine learning based NLP systems, LingPipe, GATE and BANNER, each implementing a distinct supervised machine learning method, hidden Markov models, support vector machines and conditional random fields, respectively. Results: Machine learning systems recognized laboratory test entities with moderately high recall, but low precision rates. Their recall rates were relatively higher when the number of distinct entity values (e.g., the spectrum of specimens) was very limited or when lexical morphology of the entity was distinctive (as in units of measures), yet SIE outperformed them with statistically significant margins on extracting specimen, analyte and detection limit information in both precision and F-measure. Its high recall performance was statistically significant on analyte information extraction. Conclusions: Despite its shortcomings against machine learning methods, a well-tailored symbolic system may better discern relevancy among a pile of information of the same type and may outperform a machine learning system by tapping into lexically non-local contextual information such as the document structure. PMID:24083058

ESWR1-CREM Fusion in an Intracranial Myxoid Angiomatoid Fibrous Histiocytoma-Like Tumor: A Case Report and Literature Review.

PubMed

Gareton, Albane; Pierron, Gaëlle; Mokhtari, Karima; Tran, Suzanne; Tauziède-Espariat, Arnault; Pallud, Johan; Louvel, Guillaume; Meary, Eric; Capelle, Laurent; Chrétien, Fabrice; Varlet, Pascale

2018-05-19

Gene fusions of EWSR1 with members of the CREB family of transcription factors (CREB1, ATF1, and CREM) have recently been described in exceptional intracranial myxoid mesenchymal tumors. Although this is a known gene fusion found in various mesenchymal tumors, EWSR1 fusion with CREM has only been observed in 3 intracranial myxoid tumors. In this paper, we present 1 such tumor with in-depth histopathological description and long-term follow-up. There is controversy regarding whether these tumors represent a novel entity or simply an intracranial localization of the myxoid variant of angiomatoid fibrous histiocytoma, a rare soft tissue tumor of the extremities. Out of 11 cases mentioned in the literature, the 3 isolated case reports by Dunham et al, Ochalski et al, and Alshareef et al are designated as angiomatoid fibrous histiocytoma, whereas the others are defined as a novel tumoral entity called intracranial myxoid mesenchymal tumor with EWSR1-CREB fusion. We believe the vast morphological and immunohistochemical spectrum of angiomatoid fibrous histiocytoma makes it difficult to dismiss this diagnosis.

Semi-Automated Annotation of Biobank Data Using Standard Medical Terminologies in a Graph Database.

PubMed

Hofer, Philipp; Neururer, Sabrina; Goebel, Georg

2016-01-01

Data describing biobank resources frequently contains unstructured free-text information or insufficient coding standards. (Bio-) medical ontologies like Orphanet Rare Diseases Ontology (ORDO) or the Human Disease Ontology (DOID) provide a high number of concepts, synonyms and entity relationship properties. Such standard terminologies increase quality and granularity of input data by adding comprehensive semantic background knowledge from validated entity relationships. Moreover, cross-references between terminology concepts facilitate data integration across databases using different coding standards. In order to encourage the use of standard terminologies, our aim is to identify and link relevant concepts with free-text diagnosis inputs within a biobank registry. Relevant concepts are selected automatically by lexical matching and SPARQL queries against a RDF triplestore. To ensure correctness of annotations, proposed concepts have to be confirmed by medical data administration experts before they are entered into the registry database. Relevant (bio-) medical terminologies describing diseases and phenotypes were identified and stored in a graph database which was tied to a local biobank registry. Concept recommendations during data input trigger a structured description of medical data and facilitate data linkage between heterogeneous systems.

Information and organization in public health institutes: an ontology-based modeling of the entities in the reception-analysis-report phases.

PubMed

Pozza, Giandomenico; Borgo, Stefano; Oltramari, Alessandro; Contalbrigo, Laura; Marangon, Stefano

2016-09-08

Ontologies are widely used both in the life sciences and in the management of public and private companies. Typically, the different offices in an organization develop their own models and related ontologies to capture specific tasks and goals. Although there might be an overall coordination, the use of distinct ontologies can jeopardize the integration of data across the organization since data sharing and reusability are sensitive to modeling choices. The paper provides a study of the entities that are typically found at the reception, analysis and report phases in public institutes in the life science domain. Ontological considerations and techniques are introduced and their implementation exemplified by studying the Istituto Zooprofilattico Sperimentale delle Venezie (IZSVe), a public veterinarian institute with different geographical locations and several laboratories. Different modeling issues are discussed like the identification and characterization of the main entities in these phases; the classification of the (types of) data; the clarification of the contexts and the roles of the involved entities. The study is based on a foundational ontology and shows how it can be extended to a comprehensive and coherent framework comprising the different institute's roles, processes and data. In particular, it shows how to use notions lying at the borderline between ontology and applications, like that of knowledge object. The paper aims to help the modeler to understand the core viewpoint of the organization and to improve data transparency. The study shows that the entities at play can be analyzed within a single ontological perspective allowing us to isolate a single ontological framework for the whole organization. This facilitates the development of coherent representations of the entities and related data, and fosters the use of integrated software for data management and reasoning across the company.

"He Hasn't Got the Real Toolkit!" Young Children's Reasoning about Real/Not-Real Status

ERIC Educational Resources Information Center

Bunce, Louise; Harris, Margaret

2013-01-01

During the preschool years, children develop an understanding of 2 types of real/not-real distinctions: ontological status and authenticity (Bunce & Harris, 2008). Two studies compared 3- to 5-year-old children's real/not-real judgments and justifications for 3 types of contrast involving a real entity and either a fictional character, a child…

An Exploratory Study of the Effect of Enclosed Structure on Type Design with Fixation Dispersion: Evidence from Eye Movements

ERIC Educational Resources Information Center

Ma, Min-Yuan; Chuang, Hsien-Chih

2017-01-01

Type design is the process of re-organizing visual elements and their corresponding meanings into a new organic entity, particularly for the highly logographic Chinese characters whose intrinsic features are retained even after re-organization. Due to this advantage, designers believe that such a re-organization process will not affect Chinese…

Delayed immediate-type hypersensitivity to red meat and innards: current insights into a novel disease entity.

PubMed

Fischer, Jörg; Biedermann, Tilo

2016-01-01

The development of component-resolved diagnostics instead of whole extracts has brought about major advances in recent years. Particularly remarkable has been the identification of new disease entities based on the detection of IgE antibodies against specific individual components. In this context, delayed immediate-type hypersensitivity to red meat and innards plays a key role. This disorder is more common in German-speaking countries and likely still underdiagnosed. Affected individuals exhibit delayed type I reactions following the consumption of red meat or innards (responses to the latter are more rapid). All patients have IgE antibodies against the oligosaccharide galactose-α-1,3-galactose - alpha-gal. Those affected also have to avoid alpha-gal-containing drugs such as cetuximab or gelatin-containing colloidal solutions. Also referred to as alpha-gal syndrome, this condition is unique in that it is characterized by type I hypersensitivity to a sugar instead of a protein. Given that many patients have a history of recurrent episodes of acute urticaria or angioedema, dermatologists should be familiar with the alpha-gal syndrome. © 2015 Deutsche Dermatologische Gesellschaft (DDG). Published by John Wiley & Sons Ltd.

Schema for the LANL infrasound analysis tool, infrapy

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

Dannemann, Fransiska Kate; Marcillo, Omar Eduardo

2017-04-14

The purpose of this document is to define the schema used for the operation of the infrasound analysis tool, infrapy. The tables described by this document extend the CSS3.0 or KB core schema to include information required for the operation of infrapy. This document is divided into three sections, the first being this introduction. Section two defines eight new, infrasonic data processing-specific database tables. Both internal (ORACLE) and external formats for the attributes are defined, along with a short description of each attribute. Section three of the document shows the relationships between the different tables by using entity-relationship diagrams.

Fatal hemorrhagic cystitis induced by pelvic irradiation and cyclophosphamide therapy. Case reports and review

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

Price, W.E.; Keldahl, L.R.

The potent cytotoxic drug cyclophosphamide has been used extensively for neoplastic and non-neoplastic diseases. Patients taking this drug may have received or may be receiving pelvic irradiation concurrently. This report describes two patients who developed fatal hemorrhagic cystitis induced by pelvic irradiation and cyclophosphamide therapy. Etiology, incidence, pathologic descriptions, and diagnostic and therapeutic aspects of this entity are described. The incidence and risk of serious, life-threatening bladder hemorrhage from cyclophosphamide therapy is increased by prior or concurrent pelvic irradiation. Alternative cytotoxic, non-urotoxic chemotherapy should be used in these high-risk patients.

Nephrotic Syndrome Associated with Renal Vein Thrombosis

PubMed Central

Kang, Sung Kyew; Park, Sung Kwang

1987-01-01

The coexistence of nephrotic syndrome and renal vein thrombosis has been of medical interest since Rayer’s description in 1840. Renal vein thrombosis has been underdiagnosed because of its variable clinical and radiological findings but it becomes a more frequently recognizable clinical entity since diagnosis can be easily established by modern angiographic techniques. Generally it has been believed that renal vein thrombosis may cause nephrotic syndrome. But recent articles strongly suggest that renal vein thrombosis is a complication of the nephrotic syndrome rather than a cause. We report three cases of nephrotic syndrome associated with renal vein thrombosis. PMID:3154812

Virtual Screening Approaches towards the Discovery of Toll-Like Receptor Modulators

PubMed Central

Pérez-Regidor, Lucía; Zarioh, Malik; Ortega, Laura; Martín-Santamaría, Sonsoles

2016-01-01

This review aims to summarize the latest efforts performed in the search for novel chemical entities such as Toll-like receptor (TLR) modulators by means of virtual screening techniques. This is an emergent research field with only very recent (and successful) contributions. Identification of drug-like molecules with potential therapeutic applications for the treatment of a variety of TLR-regulated diseases has attracted considerable interest due to the clinical potential. Additionally, the virtual screening databases and computational tools employed have been overviewed in a descriptive way, widening the scope for researchers interested in the field. PMID:27618029

High Spatial Resolution MRI of Cystic Adventitial Disease of the Iliofemoral Vein Communicating with the Hip Joint

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

Michaelides, Michael, E-mail: mihalismihailidis@gmail.com; Papas, Stylianos, E-mail: vascular@drpapas.com; Pantziara, Maria, E-mail: mgpantziara@gmail.com

2013-05-14

Venous cystic adventitial disease (CAD) is an extremely rare entity, and so far less than 20 cases have been described in the literature. Herein, we describe the imaging findings of CAD of iliofemoral vein in a 51-year-old woman who presented with leg swelling with special emphasis on high spatial resolution MRI, which demonstrated communication of the cyst with the hip joint. To our knowledge, this is the first description of high spatial resolution MRI findings in venous CAD supporting a new theory about the pathogenesis of venous CAD.

[Sclerosing mucoepidermoid carcinoma with eosinophilia of the thyroid: description of a case].

PubMed

Cavazza, A; Toschi, E; Valcavi, R; Piana, S; Scotti, R; Carlinfante, G; Gardini, G

1999-02-01

A case of sclerosing mucoepidermoid carcinoma with eosinophilia of the thyroid gland is described. The patient, a 32 year-old female with Hashimoto's thyroiditis, presented with a 4 cm nodule of the right lobe of the thyroid gland. The tumour was constituted by squamoid cords infiltrating a dense fibro-jaline stroma rich in eosinophils. The patient is alive and well 14 months after surgery. The literature is briefly reviewed and the differential diagnosis is discussed. In the Author's opinion, sclerosing mucoepidermoid carcinoma with eosinophilia of the tyroid is a well defined clinicopathological entity.

Evaluation of public-private partnership contract types for roadway construction, maintenance, and rehabilitation.

DOT National Transportation Integrated Search

2015-12-31

Public-private partnerships (PPPs) in transportation infrastructure projects refer to contractual agreements formed : between a public Agency and a private sector entity to allow for greater private sector participation in project : delivery. At the ...

22 CFR 513.110 - Coverage.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) Direct awards to foreign governments or public international organizations, or transactions with foreign governments or foreign governmental entities, public international organizations, foreign government owned (in...) Relationship to other sections. This section describes the types of transactions to which a debarment or...

Random walks and diffusion on networks

NASA Astrophysics Data System (ADS)

Masuda, Naoki; Porter, Mason A.; Lambiotte, Renaud

2017-11-01

Random walks are ubiquitous in the sciences, and they are interesting from both theoretical and practical perspectives. They are one of the most fundamental types of stochastic processes; can be used to model numerous phenomena, including diffusion, interactions, and opinions among humans and animals; and can be used to extract information about important entities or dense groups of entities in a network. Random walks have been studied for many decades on both regular lattices and (especially in the last couple of decades) on networks with a variety of structures. In the present article, we survey the theory and applications of random walks on networks, restricting ourselves to simple cases of single and non-adaptive random walkers. We distinguish three main types of random walks: discrete-time random walks, node-centric continuous-time random walks, and edge-centric continuous-time random walks. We first briefly survey random walks on a line, and then we consider random walks on various types of networks. We extensively discuss applications of random walks, including ranking of nodes (e.g., PageRank), community detection, respondent-driven sampling, and opinion models such as voter models.

Multi-source and ontology-based retrieval engine for maize mutant phenotypes

PubMed Central

Green, Jason M.; Harnsomburana, Jaturon; Schaeffer, Mary L.; Lawrence, Carolyn J.; Shyu, Chi-Ren

2011-01-01

Model Organism Databases, including the various plant genome databases, collect and enable access to massive amounts of heterogeneous information, including sequence data, gene product information, images of mutant phenotypes, etc, as well as textual descriptions of many of these entities. While a variety of basic browsing and search capabilities are available to allow researchers to query and peruse the names and attributes of phenotypic data, next-generation search mechanisms that allow querying and ranking of text descriptions are much less common. In addition, the plant community needs an innovative way to leverage the existing links in these databases to search groups of text descriptions simultaneously. Furthermore, though much time and effort have been afforded to the development of plant-related ontologies, the knowledge embedded in these ontologies remains largely unused in available plant search mechanisms. Addressing these issues, we have developed a unique search engine for mutant phenotypes from MaizeGDB. This advanced search mechanism integrates various text description sources in MaizeGDB to aid a user in retrieving desired mutant phenotype information. Currently, descriptions of mutant phenotypes, loci and gene products are utilized collectively for each search, though expansion of the search mechanism to include other sources is straightforward. The retrieval engine, to our knowledge, is the first engine to exploit the content and structure of available domain ontologies, currently the Plant and Gene Ontologies, to expand and enrich retrieval results in major plant genomic databases. Database URL: http:www.PhenomicsWorld.org/QBTA.php PMID:21558151

Torrance type of lethal neonatal short-limbed platyspondylic dwarfism.

PubMed

Kaibara, N; Yokoyama, K; Nakano, H

1983-01-01

A rare case of lethal neonatal short-limbed platyspondylic dwarfism is described. Roentgenographic features of this case, distinctly different from those of the classical thanatophoric dysplasia, are indistinguishable from the other three types of short-limbed platyspondylic dwarfism. Histologic features of the cartilage in this case are not very different from those of the Torrance type, but the presence of focal disruption of column formation in this case suggests a wider spectrum for this entity.

Pure spinal multiple sclerosis: A possible novel entity within the multiple sclerosis disease spectrum.

PubMed

Schee, Jie Ping; Viswanathan, Shanthi

2018-05-01

We identified five female patients retrospectively with relapsing short-segment partial myelitis whose clinical and paraclinical features were suggestive of cord involvement of multiple sclerosis (MS)-type albeit not rigidly fulfilling the 2017 McDonald criteria. Notably, these patients had not developed any typical MS-like brain lesions despite repeated neuroimaging assessments over years. Comprehensive work-up for differential diagnoses of MS and other causes of transverse myelitis particularly neuromyelitis optica spectrum disorders had been consistently negative on longitudinal follow-up. Thus, we postulate a possible entity of pure spinal MS which may represent a novel forme fruste within the MS disease spectrum.

A novel data storage logic in the cloud

PubMed Central

Mátyás, Bence; Szarka, Máté; Járvás, Gábor; Kusper, Gábor; Argay, István; Fialowski, Alice

2016-01-01

Databases which store and manage long-term scientific information related to life science are used to store huge amount of quantitative attributes. Introduction of a new entity attribute requires modification of the existing data tables and the programs that use these data tables. The solution is increasing the virtual data tables while the number of screens remains the same. The main objective of the present study was to introduce a logic called Joker Tao (JT) which provides universal data storage for cloud-based databases. It means all types of input data can be interpreted as an entity and attribute at the same time, in the same data table. PMID:29026521

A novel data storage logic in the cloud.

PubMed

Mátyás, Bence; Szarka, Máté; Járvás, Gábor; Kusper, Gábor; Argay, István; Fialowski, Alice

2016-01-01

Databases which store and manage long-term scientific information related to life science are used to store huge amount of quantitative attributes. Introduction of a new entity attribute requires modification of the existing data tables and the programs that use these data tables. The solution is increasing the virtual data tables while the number of screens remains the same. The main objective of the present study was to introduce a logic called Joker Tao (JT) which provides universal data storage for cloud-based databases. It means all types of input data can be interpreted as an entity and attribute at the same time, in the same data table.

78 FR 56657 - Notice of Solicitation of Applications for Allocation of Tariff Rate Quotas on the Import of...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-13

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Using the CDC Worksite Health ScoreCard to Assess Employer Health Promotion Efforts: A Case Study at Johns Hopkins Medicine.

PubMed

Safeer, Richard; Bowen, Wendy; Maung, Zaw; Lucik, Meg

2018-02-01

The aim of this study was to determine whether the Centers for Disease Control and Prevention Worksite Health ScoreCard (ScoreCard) is an effective vehicle for measuring workplace health promotion programs and causing change in a large employer with multiple entities defined by different physical environments and types of workers. Johns Hopkins Medicine (JHM) representatives completed a baseline ScoreCard for each of their entities. In the subsequent year, improvement of the ScoreCard was tied to leadership performance evaluation. JHM year over year scores were analyzed, along with comparisons to national benchmarks. Eleven of the 12 JHM entities improved their overall score from year one to year two and the JHM enterprise surpassed national benchmarks in year two. Organizations can use the ScoreCard as an effective measurement tool and as a method to improve the number of evidenced-based health promotion strategies provided to their employees.

14 CFR 21.97 - Approval of major changes in type design.

Code of Federal Regulations, 2011 CFR

2011-01-01

... necessary descriptive data for inclusion in the type design the other configurations of the same engine type... for approval of a major change in type design must— (1) Provide substantiating data and necessary descriptive data for inclusion in the type design; (2) Show that the changed product complies with the...

[A multidiscipline clinical and biological approach to the study of psychotic types of autistic spectrum disorders in children].

PubMed

Simashkova, N V; Iakupova, L P; Kliushnik, T P; Koval'-Zaĭtsev, A A

2013-01-01

The current problem of heterogeneity of psychotic types of autistic spectrum disorders (ASD) is reviewed. The authors present results of a multidiscipline psychopathological, pathopsychological, neurophysiological and immunological examination of 87 patients, aged from 3 to 14 years, with psychotic types of ASD: childhood psychosis (CP) and atypical childhood psychosis (ACP). Significant differences in clinical presentations of CP and ACP that were correlated with pathopsychological, neurophysiological and immunological disorders were found. These findings support different nosological entities of these types of ASD.

Improving the Accuracy of Attribute Extraction using the Relatedness between Attribute Values

NASA Astrophysics Data System (ADS)

Bollegala, Danushka; Tani, Naoki; Ishizuka, Mitsuru

Extracting attribute-values related to entities from web texts is an important step in numerous web related tasks such as information retrieval, information extraction, and entity disambiguation (namesake disambiguation). For example, for a search query that contains a personal name, we can not only return documents that contain that personal name, but if we have attribute-values such as the organization for which that person works, we can also suggest documents that contain information related to that organization, thereby improving the user's search experience. Despite numerous potential applications of attribute extraction, it remains a challenging task due to the inherent noise in web data -- often a single web page contains multiple entities and attributes. We propose a graph-based approach to select the correct attribute-values from a set of candidate attribute-values extracted for a particular entity. First, we build an undirected weighted graph in which, attribute-values are represented by nodes, and the edge that connects two nodes in the graph represents the degree of relatedness between the corresponding attribute-values. Next, we find the maximum spanning tree of this graph that connects exactly one attribute-value for each attribute-type. The proposed method outperforms previously proposed attribute extraction methods on a dataset that contains 5000 web pages.

The Application of the Weighted k-Partite Graph Problem to the Multiple Alignment for Metabolic Pathways.

PubMed

Chen, Wenbin; Hendrix, William; Samatova, Nagiza F

2017-12-01

The problem of aligning multiple metabolic pathways is one of very challenging problems in computational biology. A metabolic pathway consists of three types of entities: reactions, compounds, and enzymes. Based on similarities between enzymes, Tohsato et al. gave an algorithm for aligning multiple metabolic pathways. However, the algorithm given by Tohsato et al. neglects the similarities among reactions, compounds, enzymes, and pathway topology. How to design algorithms for the alignment problem of multiple metabolic pathways based on the similarity of reactions, compounds, and enzymes? It is a difficult computational problem. In this article, we propose an algorithm for the problem of aligning multiple metabolic pathways based on the similarities among reactions, compounds, enzymes, and pathway topology. First, we compute a weight between each pair of like entities in different input pathways based on the entities' similarity score and topological structure using Ay et al.'s methods. We then construct a weighted k-partite graph for the reactions, compounds, and enzymes. We extract a mapping between these entities by solving the maximum-weighted k-partite matching problem by applying a novel heuristic algorithm. By analyzing the alignment results of multiple pathways in different organisms, we show that the alignments found by our algorithm correctly identify common subnetworks among multiple pathways.

A knowledge based approach to matching human neurodegenerative disease and animal models

PubMed Central

Maynard, Sarah M.; Mungall, Christopher J.; Lewis, Suzanna E.; Imam, Fahim T.; Martone, Maryann E.

2013-01-01

Neurodegenerative diseases present a wide and complex range of biological and clinical features. Animal models are key to translational research, yet typically only exhibit a subset of disease features rather than being precise replicas of the disease. Consequently, connecting animal to human conditions using direct data-mining strategies has proven challenging, particularly for diseases of the nervous system, with its complicated anatomy and physiology. To address this challenge we have explored the use of ontologies to create formal descriptions of structural phenotypes across scales that are machine processable and amenable to logical inference. As proof of concept, we built a Neurodegenerative Disease Phenotype Ontology (NDPO) and an associated Phenotype Knowledge Base (PKB) using an entity-quality model that incorporates descriptions for both human disease phenotypes and those of animal models. Entities are drawn from community ontologies made available through the Neuroscience Information Framework (NIF) and qualities are drawn from the Phenotype and Trait Ontology (PATO). We generated ~1200 structured phenotype statements describing structural alterations at the subcellular, cellular and gross anatomical levels observed in 11 human neurodegenerative conditions and associated animal models. PhenoSim, an open source tool for comparing phenotypes, was used to issue a series of competency questions to compare individual phenotypes among organisms and to determine which animal models recapitulate phenotypic aspects of the human disease in aggregate. Overall, the system was able to use relationships within the ontology to bridge phenotypes across scales, returning non-trivial matches based on common subsumers that were meaningful to a neuroscientist with an advanced knowledge of neuroanatomy. The system can be used both to compare individual phenotypes and also phenotypes in aggregate. This proof of concept suggests that expressing complex phenotypes using formal ontologies provides considerable benefit for comparing phenotypes across scales and species. PMID:23717278

Box-and-arrow explanations need not be more abstract than neuroscientific mechanism descriptions.

PubMed

Datteri, Edoardo; Laudisa, Federico

2014-01-01

The nature of the relationship between box-and-arrow (BA) explanations and neuroscientific mechanism descriptions (NMDs) is a key foundational issue for cognitive science. In this article we attempt to identify the nature of the constraints imposed by BA explanations on the formulation of NMDs. On the basis of a case study about motor control, we argue that BA explanations and NMDs both identify regularities that hold in the system, and that these regularities place constraints on the formulation of NMDs from BA analyses, and vice versa. The regularities identified in the two kinds of explanation play a crucial role in reasoning about the relationship between them, and in justifying the use of neuroscientific experimental techniques for the empirical testing of BA analyses of behavior. In addition, we make claims concerning the similarities and differences between BA analyses and NMDs. First, we argue that both types of explanation describe mechanisms. Second, we propose that they differ in terms of the theoretical vocabulary used to denote the entities and properties involved in the mechanism and engaging in regular, mutual interactions. On the contrary, the notion of abstractness, defined as omission of detail, does not help to distinguish BA analyses from NMDs: there is a sense in which BA analyses are more detailed than NMDs. In relation to this, we also focus on the nature of the extra detail included in NMDs and missing from BA analyses, arguing that such detail does not always concern how the system works. Finally, we propose reasons for doubting that BA analyses, unlike NMDs, may be considered "mechanism sketches." We have developed these views by critically analyzing recent claims in the philosophical literature regarding the foundations of cognitive science.

PrIMe Next Frontier: Large, Multi-Dimensional Data Sets

DTIC Science & Technology

2015-07-21

is provided below.  3.4.2 Entities  Figure  4  is  a  diagram  that  represents  the  datatypes   of  objects/instances  that  are  used  within  the...ajax({ type: ’GET’, url: 𔃻.html’, dataType : ’text’, success: function(res) { $(’body’).append(res... dataType : ’script’, success: function() { if (++counter == libraries.length) createSpecWindow(callback

24 CFR 214.105 - Preliminary application process.

Code of Federal Regulations, 2012 CFR

2012-04-01

... AUTHORITIES HOUSING COUNSELING PROGRAM Approval and Disapproval of Housing Counseling Agencies § 214.105... which the parent entity exercises control over the quality and type of housing counseling services... required to submit an application for HUD approval. However, to participate in HUD's Housing Counseling...

24 CFR 214.105 - Preliminary application process.

Code of Federal Regulations, 2013 CFR

2013-04-01

... AUTHORITIES HOUSING COUNSELING PROGRAM Approval and Disapproval of Housing Counseling Agencies § 214.105... which the parent entity exercises control over the quality and type of housing counseling services... required to submit an application for HUD approval. However, to participate in HUD's Housing Counseling...

24 CFR 214.105 - Preliminary application process.

Code of Federal Regulations, 2010 CFR

2010-04-01

... AUTHORITIES HOUSING COUNSELING PROGRAM Approval and Disapproval of Housing Counseling Agencies § 214.105... which the parent entity exercises control over the quality and type of housing counseling services... required to submit an application for HUD approval. However, to participate in HUD's Housing Counseling...

The benefits of looking across many cancer genomes

Cancer.gov

Cancer is not a single entity, but rather, it is more than one hundred complex and distinct diseases, with most cancer types demanding a unique treatment strategy. TCGA researchers have developed a formal project for a cross tumor analysis, called Pan-Can

Automatic recognition of disorders, findings, pharmaceuticals and body structures from clinical text: an annotation and machine learning study.

PubMed

Skeppstedt, Maria; Kvist, Maria; Nilsson, Gunnar H; Dalianis, Hercules

2014-06-01

Automatic recognition of clinical entities in the narrative text of health records is useful for constructing applications for documentation of patient care, as well as for secondary usage in the form of medical knowledge extraction. There are a number of named entity recognition studies on English clinical text, but less work has been carried out on clinical text in other languages. This study was performed on Swedish health records, and focused on four entities that are highly relevant for constructing a patient overview and for medical hypothesis generation, namely the entities: Disorder, Finding, Pharmaceutical Drug and Body Structure. The study had two aims: to explore how well named entity recognition methods previously applied to English clinical text perform on similar texts written in Swedish; and to evaluate whether it is meaningful to divide the more general category Medical Problem, which has been used in a number of previous studies, into the two more granular entities, Disorder and Finding. Clinical notes from a Swedish internal medicine emergency unit were annotated for the four selected entity categories, and the inter-annotator agreement between two pairs of annotators was measured, resulting in an average F-score of 0.79 for Disorder, 0.66 for Finding, 0.90 for Pharmaceutical Drug and 0.80 for Body Structure. A subset of the developed corpus was thereafter used for finding suitable features for training a conditional random fields model. Finally, a new model was trained on this subset, using the best features and settings, and its ability to generalise to held-out data was evaluated. This final model obtained an F-score of 0.81 for Disorder, 0.69 for Finding, 0.88 for Pharmaceutical Drug, 0.85 for Body Structure and 0.78 for the combined category Disorder+Finding. The obtained results, which are in line with or slightly lower than those for similar studies on English clinical text, many of them conducted using a larger training data set, show that the approaches used for English are also suitable for Swedish clinical text. However, a small proportion of the errors made by the model are less likely to occur in English text, showing that results might be improved by further tailoring the system to clinical Swedish. The entity recognition results for the individual entities Disorder and Finding show that it is meaningful to separate the general category Medical Problem into these two more granular entity types, e.g. for knowledge mining of co-morbidity relations and disorder-finding relations. Copyright © 2014 The Authors. Published by Elsevier Inc. All rights reserved.

Active learning for ontological event extraction incorporating named entity recognition and unknown word handling.

PubMed

Han, Xu; Kim, Jung-jae; Kwoh, Chee Keong

2016-01-01

Biomedical text mining may target various kinds of valuable information embedded in the literature, but a critical obstacle to the extension of the mining targets is the cost of manual construction of labeled data, which are required for state-of-the-art supervised learning systems. Active learning is to choose the most informative documents for the supervised learning in order to reduce the amount of required manual annotations. Previous works of active learning, however, focused on the tasks of entity recognition and protein-protein interactions, but not on event extraction tasks for multiple event types. They also did not consider the evidence of event participants, which might be a clue for the presence of events in unlabeled documents. Moreover, the confidence scores of events produced by event extraction systems are not reliable for ranking documents in terms of informativity for supervised learning. We here propose a novel committee-based active learning method that supports multi-event extraction tasks and employs a new statistical method for informativity estimation instead of using the confidence scores from event extraction systems. Our method is based on a committee of two systems as follows: We first employ an event extraction system to filter potential false negatives among unlabeled documents, from which the system does not extract any event. We then develop a statistical method to rank the potential false negatives of unlabeled documents 1) by using a language model that measures the probabilities of the expression of multiple events in documents and 2) by using a named entity recognition system that locates the named entities that can be event arguments (e.g. proteins). The proposed method further deals with unknown words in test data by using word similarity measures. We also apply our active learning method for the task of named entity recognition. We evaluate the proposed method against the BioNLP Shared Tasks datasets, and show that our method can achieve better performance than such previous methods as entropy and Gibbs error based methods and a conventional committee-based method. We also show that the incorporation of named entity recognition into the active learning for event extraction and the unknown word handling further improve the active learning method. In addition, the adaptation of the active learning method into named entity recognition tasks also improves the document selection for manual annotation of named entities.

The contribution of the left anterior ventrolateral temporal lobe to the retrieval of personal semantics.

PubMed

Grilli, Matthew D; Bercel, John J; Wank, Aubrey A; Rapcsak, Steven Z

2018-06-04

Autobiographical facts and personal trait knowledge are conceptualized as distinct types of personal semantics, but the cognitive and neural mechanisms that separate them remain underspecified. One distinction may be their level of specificity, with autobiographical facts reflecting idiosyncratic conceptual knowledge and personal traits representing basic level category knowledge about the self. Given the critical role of the left anterior ventrolateral temporal lobe (AVTL) in the storage and retrieval of semantic information about unique entities, we hypothesized that knowledge of autobiographical facts may depend on the integrity of this region to a greater extent than personal traits. To provide neuropsychological evidence relevant to this issue, we investigated personal semantics, semantic knowledge of non-personal unique entities, and episodic memory in two individuals with well-defined left (MK) versus right (DW) AVTL lesions. Relative to controls, MK demonstrated preserved personal trait knowledge but impaired "experience-far" (i.e., spatiotemporal independent) autobiographical fact knowledge, semantic memory for non-personal unique entities, and episodic memory. In contrast, both experience-far autobiographical facts and personal traits were spared in DW, whereas episodic memory and aspects of semantic memory for non-personal unique entities were impaired. These findings support the notion that autobiographical facts and personal traits have distinct cognitive features and neural mechanisms. They also suggest a common organizing principle for personal and non-personal semantics, namely the specificity of such knowledge to an entity, which is reflected in the contribution of the left AVTL to retrieval. Copyright © 2018 Elsevier Ltd. All rights reserved.

Encoding of Fundamental Chemical Entities of Organic Reactivity Interest using chemical ontology and XML.

PubMed

Durairaj, Vijayasarathi; Punnaivanam, Sankar

2015-09-01

Fundamental chemical entities are identified in the context of organic reactivity and classified as appropriate concept classes namely ElectronEntity, AtomEntity, AtomGroupEntity, FunctionalGroupEntity and MolecularEntity. The entity classes and their subclasses are organized into a chemical ontology named "ChemEnt" for the purpose of assertion, restriction and modification of properties through entity relations. Individual instances of entity classes are defined and encoded as a library of chemical entities in XML. The instances of entity classes are distinguished with a unique notation and identification values in order to map them with the ontology definitions. A model GUI named Entity Table is created to view graphical representations of all the entity instances. The detection of chemical entities in chemical structures is achieved through suitable algorithms. The possibility of asserting properties to the entities at different levels and the mechanism of property flow within the hierarchical entity levels is outlined. Copyright © 2015 Elsevier Inc. All rights reserved.

Data-Driven Information Extraction from Chinese Electronic Medical Records

PubMed Central

Zhao, Tianwan; Ge, Chen; Gao, Weiguo; Wei, Jia; Zhu, Kenny Q.

2015-01-01

Objective This study aims to propose a data-driven framework that takes unstructured free text narratives in Chinese Electronic Medical Records (EMRs) as input and converts them into structured time-event-description triples, where the description is either an elaboration or an outcome of the medical event. Materials and Methods Our framework uses a hybrid approach. It consists of constructing cross-domain core medical lexica, an unsupervised, iterative algorithm to accrue more accurate terms into the lexica, rules to address Chinese writing conventions and temporal descriptors, and a Support Vector Machine (SVM) algorithm that innovatively utilizes Normalized Google Distance (NGD) to estimate the correlation between medical events and their descriptions. Results The effectiveness of the framework was demonstrated with a dataset of 24,817 de-identified Chinese EMRs. The cross-domain medical lexica were capable of recognizing terms with an F1-score of 0.896. 98.5% of recorded medical events were linked to temporal descriptors. The NGD SVM description-event matching achieved an F1-score of 0.874. The end-to-end time-event-description extraction of our framework achieved an F1-score of 0.846. Discussion In terms of named entity recognition, the proposed framework outperforms state-of-the-art supervised learning algorithms (F1-score: 0.896 vs. 0.886). In event-description association, the NGD SVM is superior to SVM using only local context and semantic features (F1-score: 0.874 vs. 0.838). Conclusions The framework is data-driven, weakly supervised, and robust against the variations and noises that tend to occur in a large corpus. It addresses Chinese medical writing conventions and variations in writing styles through patterns used for discovering new terms and rules for updating the lexica. PMID:26295801

Data-Driven Information Extraction from Chinese Electronic Medical Records.

PubMed

Xu, Dong; Zhang, Meizhuo; Zhao, Tianwan; Ge, Chen; Gao, Weiguo; Wei, Jia; Zhu, Kenny Q

2015-01-01

This study aims to propose a data-driven framework that takes unstructured free text narratives in Chinese Electronic Medical Records (EMRs) as input and converts them into structured time-event-description triples, where the description is either an elaboration or an outcome of the medical event. Our framework uses a hybrid approach. It consists of constructing cross-domain core medical lexica, an unsupervised, iterative algorithm to accrue more accurate terms into the lexica, rules to address Chinese writing conventions and temporal descriptors, and a Support Vector Machine (SVM) algorithm that innovatively utilizes Normalized Google Distance (NGD) to estimate the correlation between medical events and their descriptions. The effectiveness of the framework was demonstrated with a dataset of 24,817 de-identified Chinese EMRs. The cross-domain medical lexica were capable of recognizing terms with an F1-score of 0.896. 98.5% of recorded medical events were linked to temporal descriptors. The NGD SVM description-event matching achieved an F1-score of 0.874. The end-to-end time-event-description extraction of our framework achieved an F1-score of 0.846. In terms of named entity recognition, the proposed framework outperforms state-of-the-art supervised learning algorithms (F1-score: 0.896 vs. 0.886). In event-description association, the NGD SVM is superior to SVM using only local context and semantic features (F1-score: 0.874 vs. 0.838). The framework is data-driven, weakly supervised, and robust against the variations and noises that tend to occur in a large corpus. It addresses Chinese medical writing conventions and variations in writing styles through patterns used for discovering new terms and rules for updating the lexica.

Towards a conceptual multi-agent-based framework to simulate the spatial group decision-making process

NASA Astrophysics Data System (ADS)

Ghavami, Seyed Morsal; Taleai, Mohammad

2017-04-01

Most spatial problems are multi-actor, multi-issue and multi-phase in nature. In addition to their intrinsic complexity, spatial problems usually involve groups of actors from different organizational and cognitive backgrounds, all of whom participate in a social structure to resolve or reduce the complexity of a given problem. Hence, it is important to study and evaluate what different aspects influence the spatial problem resolution process. Recently, multi-agent systems consisting of groups of separate agent entities all interacting with each other have been put forward as appropriate tools to use to study and resolve such problems. In this study, then in order to generate a better level of understanding regarding the spatial problem group decision-making process, a conceptual multi-agent-based framework is used that represents and specifies all the necessary concepts and entities needed to aid group decision making, based on a simulation of the group decision-making process as well as the relationships that exist among the different concepts involved. The study uses five main influencing entities as concepts in the simulation process: spatial influence, individual-level influence, group-level influence, negotiation influence and group performance measures. Further, it explains the relationship among different concepts in a descriptive rather than explanatory manner. To illustrate the proposed framework, the approval process for an urban land use master plan in Zanjan—a provincial capital in Iran—is simulated using MAS, the results highlighting the effectiveness of applying an MAS-based framework when wishing to study the group decision-making process used to resolve spatial problems.

Heterogeneity in Waardenburg syndrome.

PubMed Central

Hageman, M J; Delleman, J W

1977-01-01

Heterogeneity of Waardenburg syndrome is demonstrated in a review of 1,285 patients from the literature and 34 previously unreported patients in five families in the Netherlands. The syndrome seems to consist of two genetically distinct entities that can be differentiated clinically: type I, Waardenburg syndrome with dystopia canthorum; and type II, Waardenburg syndrome without dystopia canthorum. Both types have an autosomal dominant mode of inheritance. The incidence of bilateral deafness in the two types of the syndrome was found in one-fourth with type I and about half of the patients with type II. This difference has important consequences for genetic counseling. Images Fig. 7 Fig. 8 Fig. 9 PMID:331943

cMapper: gene-centric connectivity mapper for EBI-RDF platform.

PubMed

Shoaib, Muhammad; Ansari, Adnan Ahmad; Ahn, Sung-Min

2017-01-15

In this era of biological big data, data integration has become a common task and a challenge for biologists. The Resource Description Framework (RDF) was developed to enable interoperability of heterogeneous datasets. The EBI-RDF platform enables an efficient data integration of six independent biological databases using RDF technologies and shared ontologies. However, to take advantage of this platform, biologists need to be familiar with RDF technologies and SPARQL query language. To overcome this practical limitation of the EBI-RDF platform, we developed cMapper, a web-based tool that enables biologists to search the EBI-RDF databases in a gene-centric manner without a thorough knowledge of RDF and SPARQL. cMapper allows biologists to search data entities in the EBI-RDF platform that are connected to genes or small molecules of interest in multiple biological contexts. The input to cMapper consists of a set of genes or small molecules, and the output are data entities in six independent EBI-RDF databases connected with the given genes or small molecules in the user's query. cMapper provides output to users in the form of a graph in which nodes represent data entities and the edges represent connections between data entities and inputted set of genes or small molecules. Furthermore, users can apply filters based on database, taxonomy, organ and pathways in order to focus on a core connectivity graph of their interest. Data entities from multiple databases are differentiated based on background colors. cMapper also enables users to investigate shared connections between genes or small molecules of interest. Users can view the output graph on a web browser or download it in either GraphML or JSON formats. cMapper is available as a web application with an integrated MySQL database. The web application was developed using Java and deployed on Tomcat server. We developed the user interface using HTML5, JQuery and the Cytoscape Graph API. cMapper can be accessed at http://cmapper.ewostech.net Readers can download the development manual from the website http://cmapper.ewostech.net/docs/cMapperDocumentation.pdf. Source Code is available at https://github.com/muhammadshoaib/cmapperContact:smahn@gachon.ac.krSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

[Predictive factors of depression in adolescents at school: the role of implicit theories of intelligence].

PubMed

Da Fonseca, D; Cury, F; Rufo, M; Poinso, F

2007-10-01

The aim of this study was to complete the identification of predictive factors of depression during adolescence. For some authors, depression is characterized by a style of attribution, which consists essentially in attributing most of the negative outcomes to internal, stable, and uncontrollable factors. It seems that these attributions depend essentially on the type of their beliefs and in particular, those concerning the nature of intelligence. These beliefs called "implicit theories of intelligence", are the entity theory of intelligence and the incremental theory of intelligence. The entity theory of intelligence corresponds to the belief according to which intelligence is the expression of a relatively stable, fixed, and noncontrollable feature, and which we cannot change. In contrast, the incremental theory corresponds to the belief according to which intelligence is a controllable quality, which we can develop through effort and work. Several studies have demonstrated that the adolescents who consider intelligence as a malleable quality explain their bad results by internal, unstable, and controllable factors. Conversely, students who consider intelligence as a fixed capacity tend to strongly attribute their failure to internal, stable, and uncontrollable factors. We have consequently formulated the hypothesis according to which the entity theory should be a predictive factor of depression. We have also tested the fact that anxiety should be a mediating factor within the relation between the entity theory and depression. The sample was composed of 424 adolescents. Using different questionnaires, we measured implicit theories of the intelligence (TIDI), self-esteem (EES), anxiety (STAI-Form Y-B) and depression (CDI). Multiple regression analyses demonstrated that the entity theory of intelligence positively predicts depression. Self-esteem negatively predicts anxiety and depression. Moreover, anxiety is a mediator of the relation between self-esteem and depression, on one hand, and the relation between the entity theory of intelligence and depression, on the other. Finally, the effect of the entity theory of intelligence appears to be modulated by the level of self-esteem. This study explains the mechanisms by which the implicit theories of intelligence engender anxiety and depression. Furthermore, this approach provides interesting perspectives in the prevention and management of adolescents presenting depression.

Oncologic principles in breast reconstruction.

PubMed

Cho, B C John; McCready, David R

2007-01-01

Breast cancer is the most common malignancy in North American women. Although the incidence has risen over the last 20 years, mortality rates appear to be decreasing, possibly as a result of earlier detection and more effective therapy. Breast cancer is a heterogeneous group of conditions that can be divided into the noninvasive entities of lobular carcinoma in situ (LCIS) and ductal carcinoma-in-situ (DCIS), and invasive cancers. In this article, the spectrum of breast cancer is presented from the noninvasive entities, through invasive breast cancer types, to advanced and recurrent cancer. The rationales for current treatment options are presented. Evidence is presented for current adjuvant treatment options, and the rationale for surgical decision-making is presented.

14 CFR 21.97 - Approval of major changes in type design.

Code of Federal Regulations, 2012 CFR

2012-01-01

... must— (1) Provide substantiating data and necessary descriptive data for inclusion in the type design... is made unless the applicant identifies in the necessary descriptive data for inclusion in the type... 14 Aeronautics and Space 1 2012-01-01 2012-01-01 false Approval of major changes in type design...

14 CFR 21.97 - Approval of major changes in type design.

Code of Federal Regulations, 2013 CFR

2013-01-01

.... (a) An applicant for approval of a major change in type design must— (1) Provide substantiating data and necessary descriptive data for inclusion in the type design; (2) Show that the changed product... the necessary descriptive data for inclusion in the type design the other configurations of the same...

14 CFR 21.97 - Approval of major changes in type design.

Code of Federal Regulations, 2010 CFR

2010-01-01

... must submit substantiating data and necessary descriptive data for inclusion in the type design. (b... major change in type design must— (1) Provide substantiating data and necessary descriptive data for... 14 Aeronautics and Space 1 2010-01-01 2010-01-01 false Approval of major changes in type design...

Technical architecture of ONC-approved plans for statewide health information exchange.

PubMed

Barrows, Randolph C; Ezzard, John

2011-01-01

ONC-approved state plans for HIE were reviewed for descriptions and depictions of statewide HIE technical architecture. Review was complicated by non-standard organizational elements and technical terminology across state plans. Findings were mapped to industry standard, referenced, and defined HIE architecture descriptions and characteristics. Results are preliminary due to the initial subset of ONC-approved plans available, the rapid pace of new ONC-plan approvals, and continuing advancements in standards and technology of HIE, etc. Review of 28 state plans shows virtually all include a direct messaging component, but for participating entities at state-specific levels of granularity (RHIO, enterprise, organization/provider). About ½ of reviewed plans describe a federated architecture, and ¼ of plans utilize a single-vendor "hybrid-federated" architecture. About 1/3 of states plan to leverage new federal and open exchange technologies (DIRECT, CONNECT, etc.). Only one plan describes a centralized architecture for statewide HIE, but others combine central and federated architectural approaches.

Multi-Infarct Dementia: A Historical Perspective.

PubMed

McKay, Erin; Counts, Scott E

2017-01-01

Multi-infarct dementia (MID), a prominent subtype of vascular dementia (VaD), has only achieved recognition in the last 4 decades. Since its original description, the characterization, etiological understanding, and therapeutic direction of MID and other VaD subtypes has progressed at an astounding rate. This paper divides the landmark discoveries and emergence of new research strategies for MID into decade-defining patterns so that a condensed picture of the total history of MID and its eventual inclusion as a VaD subtype emerges. This paper follows the first descriptive decade, a shift to a preventative focus, a renewed interest coinciding with timely advances in research technology, and a hopeful return to treatment possibilities for VaD. Concisely tracing the historical lineage of the modern understanding of MID, both as a singular entity and as part of the VaD con-stellation of disorders, provides a novel perspective on the foundation upon which future advances in combating vascular contributions to dementia will be based.

Computer modeling describes gravity-related adaptation in cell cultures.

PubMed

Alexandrov, Ludmil B; Alexandrova, Stoyana; Usheva, Anny

2009-12-16

Questions about the changes of biological systems in response to hostile environmental factors are important but not easy to answer. Often, the traditional description with differential equations is difficult due to the overwhelming complexity of the living systems. Another way to describe complex systems is by simulating them with phenomenological models such as the well-known evolutionary agent-based model (EABM). Here we developed an EABM to simulate cell colonies as a multi-agent system that adapts to hyper-gravity in starvation conditions. In the model, the cell's heritable characteristics are generated and transferred randomly to offspring cells. After a qualitative validation of the model at normal gravity, we simulate cellular growth in hyper-gravity conditions. The obtained data are consistent with previously confirmed theoretical and experimental findings for bacterial behavior in environmental changes, including the experimental data from the microgravity Atlantis and the Hypergravity 3000 experiments. Our results demonstrate that it is possible to utilize an EABM with realistic qualitative description to examine the effects of hypergravity and starvation on complex cellular entities.

Production of Referring Expressions for an Unknown Audience: A Computational Model of Communal Common Ground

PubMed Central

Kutlak, Roman; van Deemter, Kees; Mellish, Chris

2016-01-01

This article presents a computational model of the production of referring expressions under uncertainty over the hearer's knowledge. Although situations where the hearer's knowledge is uncertain have seldom been addressed in the computational literature, they are common in ordinary communication, for example when a writer addresses an unknown audience, or when a speaker addresses a stranger. We propose a computational model composed of three complimentary heuristics based on, respectively, an estimation of the recipient's knowledge, an estimation of the extent to which a property is unexpected, and the question of what is the optimum number of properties in a given situation. The model was tested in an experiment with human readers, in which it was compared against the Incremental Algorithm and human-produced descriptions. The results suggest that the new model outperforms the Incremental Algorithm in terms of the proportion of correctly identified entities and in terms of the perceived quality of the generated descriptions. PMID:27630592

An avionics scenario and command model description for Space Generic Open Avionics Architecture (SGOAA)

NASA Technical Reports Server (NTRS)

Stovall, John R.; Wray, Richard B.

1994-01-01

This paper presents a description of a model for a space vehicle operational scenario and the commands for avionics. This model will be used in developing a dynamic architecture simulation model using the Statemate CASE tool for validation of the Space Generic Open Avionics Architecture (SGOAA). The SGOAA has been proposed as an avionics architecture standard to NASA through its Strategic Avionics Technology Working Group (SATWG) and has been accepted by the Society of Automotive Engineers (SAE) for conversion into an SAE Avionics Standard. This architecture was developed for the Flight Data Systems Division (FDSD) of the NASA Johnson Space Center (JSC) by the Lockheed Engineering and Sciences Company (LESC), Houston, Texas. This SGOAA includes a generic system architecture for the entities in spacecraft avionics, a generic processing external and internal hardware architecture, and a nine class model of interfaces. The SGOAA is both scalable and recursive and can be applied to any hierarchical level of hardware/software processing systems.

Technical Architecture of ONC-Approved Plans For Statewide Health Information Exchange

PubMed Central

Barrows, Randolph C.; Ezzard, John

2011-01-01

ONC-approved state plans for HIE were reviewed for descriptions and depictions of statewide HIE technical architecture. Review was complicated by non-standard organizational elements and technical terminology across state plans. Findings were mapped to industry standard, referenced, and defined HIE architecture descriptions and characteristics. Results are preliminary due to the initial subset of ONC-approved plans available, the rapid pace of new ONC-plan approvals, and continuing advancements in standards and technology of HIE, etc. Review of 28 state plans shows virtually all include a direct messaging component, but for participating entities at state-specific levels of granularity (RHIO, enterprise, organization/provider). About ½ of reviewed plans describe a federated architecture, and ¼ of plans utilize a single-vendor “hybrid-federated” architecture. About 1/3 of states plan to leverage new federal and open exchange technologies (DIRECT, CONNECT, etc.). Only one plan describes a centralized architecture for statewide HIE, but others combine central and federated architectural approaches. PMID:22195059

Feasibility study of developing and creating a standardized subset of bridge plans.

DOT National Transportation Integrated Search

2015-09-01

This study investigated sizes and geometry of existing bridges in Colorado and investigated standard bridge systems used by : other entities. The study proposed standard bridge types advancing the goals of SHRP 2 R19A & B, the rapidest ABC : construc...

77 FR 40344 - Procurement List; Proposed Additions and Deletion

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-09

... will not result in any additional reporting, recordkeeping or other compliance requirements for small.... If approved, the action will result in authorizing small entities to furnish the product and services...--Rock Island, Rock Island, IL. Services Service Type/Location: Contact Center Services, Defense Manpower...

28 CFR 35.160 - General.

Code of Federal Regulations, 2010 CFR

2010-07-01

... Administration DEPARTMENT OF JUSTICE NONDISCRIMINATION ON THE BASIS OF DISABILITY IN STATE AND LOCAL GOVERNMENT... communications with applicants, participants, and members of the public with disabilities are as effective as... benefits of, a service, program, or activity conducted by a public entity. (2) In determining what type of...

The Modular Instrumentation Family: Defense and Industry Applications

DTIC Science & Technology

2015-02-01

commercial industry systems. The author can be contacted at gerome.q.banks.civ@mail.mil. Boeing 747 undergoing cargo hold vulnerability testing at Aberdeen...state and local governments, allied foreign governments and commercial entities. Conse- quently, ADMAS models are designed for various types of

Variation in Relations with Environmental Publics.

ERIC Educational Resources Information Center

Grunig, Larissa A.

1987-01-01

Examines how successful public relations practitioners are in dealing with pressure groups and the government. Compares their relationship with key publics and the relationship they enjoy with other, perhaps less threatening entities such as suppliers, the media, and stockholders. Compares relationships across types of organizations. (NKA)

75 FR 29718 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-05-27

... Environmental Questionnaire and Checklist. OMB Control Number: 0690-0028. Form Number(s): CD-593. Type of...: 400. Needs and Uses: The Environmental Questionnaire and Checklist is designed to be used by both grants applicants and Federal entities proposing construction or infrastructure projects. The questions...

DNA methylation-based classification of central nervous system tumours.

PubMed

Capper, David; Jones, David T W; Sill, Martin; Hovestadt, Volker; Schrimpf, Daniel; Sturm, Dominik; Koelsche, Christian; Sahm, Felix; Chavez, Lukas; Reuss, David E; Kratz, Annekathrin; Wefers, Annika K; Huang, Kristin; Pajtler, Kristian W; Schweizer, Leonille; Stichel, Damian; Olar, Adriana; Engel, Nils W; Lindenberg, Kerstin; Harter, Patrick N; Braczynski, Anne K; Plate, Karl H; Dohmen, Hildegard; Garvalov, Boyan K; Coras, Roland; Hölsken, Annett; Hewer, Ekkehard; Bewerunge-Hudler, Melanie; Schick, Matthias; Fischer, Roger; Beschorner, Rudi; Schittenhelm, Jens; Staszewski, Ori; Wani, Khalida; Varlet, Pascale; Pages, Melanie; Temming, Petra; Lohmann, Dietmar; Selt, Florian; Witt, Hendrik; Milde, Till; Witt, Olaf; Aronica, Eleonora; Giangaspero, Felice; Rushing, Elisabeth; Scheurlen, Wolfram; Geisenberger, Christoph; Rodriguez, Fausto J; Becker, Albert; Preusser, Matthias; Haberler, Christine; Bjerkvig, Rolf; Cryan, Jane; Farrell, Michael; Deckert, Martina; Hench, Jürgen; Frank, Stephan; Serrano, Jonathan; Kannan, Kasthuri; Tsirigos, Aristotelis; Brück, Wolfgang; Hofer, Silvia; Brehmer, Stefanie; Seiz-Rosenhagen, Marcel; Hänggi, Daniel; Hans, Volkmar; Rozsnoki, Stephanie; Hansford, Jordan R; Kohlhof, Patricia; Kristensen, Bjarne W; Lechner, Matt; Lopes, Beatriz; Mawrin, Christian; Ketter, Ralf; Kulozik, Andreas; Khatib, Ziad; Heppner, Frank; Koch, Arend; Jouvet, Anne; Keohane, Catherine; Mühleisen, Helmut; Mueller, Wolf; Pohl, Ute; Prinz, Marco; Benner, Axel; Zapatka, Marc; Gottardo, Nicholas G; Driever, Pablo Hernáiz; Kramm, Christof M; Müller, Hermann L; Rutkowski, Stefan; von Hoff, Katja; Frühwald, Michael C; Gnekow, Astrid; Fleischhack, Gudrun; Tippelt, Stephan; Calaminus, Gabriele; Monoranu, Camelia-Maria; Perry, Arie; Jones, Chris; Jacques, Thomas S; Radlwimmer, Bernhard; Gessi, Marco; Pietsch, Torsten; Schramm, Johannes; Schackert, Gabriele; Westphal, Manfred; Reifenberger, Guido; Wesseling, Pieter; Weller, Michael; Collins, Vincent Peter; Blümcke, Ingmar; Bendszus, Martin; Debus, Jürgen; Huang, Annie; Jabado, Nada; Northcott, Paul A; Paulus, Werner; Gajjar, Amar; Robinson, Giles W; Taylor, Michael D; Jaunmuktane, Zane; Ryzhova, Marina; Platten, Michael; Unterberg, Andreas; Wick, Wolfgang; Karajannis, Matthias A; Mittelbronn, Michel; Acker, Till; Hartmann, Christian; Aldape, Kenneth; Schüller, Ulrich; Buslei, Rolf; Lichter, Peter; Kool, Marcel; Herold-Mende, Christel; Ellison, David W; Hasselblatt, Martin; Snuderl, Matija; Brandner, Sebastian; Korshunov, Andrey; von Deimling, Andreas; Pfister, Stefan M

2018-03-22

Accurate pathological diagnosis is crucial for optimal management of patients with cancer. For the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. Here we present a comprehensive approach for the DNA methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. We show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. For broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. Our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology.

Oskar Fischer and the study of dementia

PubMed Central

2009-01-01

The centenary of Alois Alzheimer's description of the case of Auguste Deter has renewed interest in the early history of dementia research. In his 1907 paper Alzheimer described the presence of plaques and tangles in one case of presenile dementia. In the same year, Oskar Fischer reported neuritic plaques in 12 cases of senile dementia. These were landmark findings in the history of research in dementia because they delineated the clinicopathological entity that is now known as Alzheimer's disease. Although much has been written about Alzheimer, only little is known about Fischer. The present article discusses Fischer's work on dementia in the context of his life and time. PMID:18952676

Current Perspectives on Primary Immunodeficiency Diseases

PubMed Central

Kumar, Arvind; Teuber, Suzanne S.; Gershwin, M. Eric

2006-01-01

Since the original description of X-linked agammaglobulinemia in 1952, the number of independent primary immunodeficiency diseases (PIDs) has expanded to more than 100 entities. By definition, a PID is a genetically determined disorder resulting in enhanced susceptibility to infectious disease. Despite the heritable nature of these diseases, some PIDs are clinically manifested only after prerequisite environmental exposures but they often have associated malignant, allergic, or autoimmune manifestations. PIDs must be distinguished from secondary or acquired immunodeficiencies, which are far more common. In this review, we will place these immunodeficiencies in the context of both clinical and laboratory presentations as well as highlight the known genetic basis. PMID:17162365

ML-Space: Hybrid Spatial Gillespie and Particle Simulation of Multi-Level Rule-Based Models in Cell Biology.

PubMed

Bittig, Arne T; Uhrmacher, Adelinde M

2017-01-01

Spatio-temporal dynamics of cellular processes can be simulated at different levels of detail, from (deterministic) partial differential equations via the spatial Stochastic Simulation algorithm to tracking Brownian trajectories of individual particles. We present a spatial simulation approach for multi-level rule-based models, which includes dynamically hierarchically nested cellular compartments and entities. Our approach ML-Space combines discrete compartmental dynamics, stochastic spatial approaches in discrete space, and particles moving in continuous space. The rule-based specification language of ML-Space supports concise and compact descriptions of models and to adapt the spatial resolution of models easily.

A rare giant scalp dermatofibrosarcoma protuberans

PubMed Central

Arifin, Muhammad Z.; Yudoyono, Farid; Dahlan, Rully H.; Hernowo, Bethy S.; Sutiono, Agung B.; Faried, Ahmad

2014-01-01

Background: Giant dermatofibrosarcoma protuberans (DFSP) of the scalp is a rare case, which is an intermediate grade soft tissue neoplasm originating from the dermal layer of the skin, which usually occurs in adults. Case Description: We describe such a case in a 26-year-old male. A wide local excision of the tumor with a generous tissue margin was performed; microscopic and immunohistochemical findings established the diagnosis of recurrent DFSP. Conclusion: Our case is unique in that it is presented as a dermatofibrosarcoma protuberans of the scalp, which is an extremely rare clinical entity, and the patient remains well after 14 months with no further treatment, without any tumor recurrence. PMID:24818052

Magnetic resonance imaging of the pediatric neck: an overview.

PubMed

Shekdar, Karuna V; Mirsky, David M; Kazahaya, Ken; Bilaniuk, Larissa T

2012-08-01

Evaluation of neck lesions in the pediatric population can be a diagnostic challenge, for which magnetic resonance (MR) imaging is extremely valuable. This article provides an overview of the value and utility of MR imaging in the evaluation of pediatric neck lesions, addressing what the referring clinician requires from the radiologist. Concise descriptions and illustrations of MR imaging findings of commonly encountered pathologic entities in the pediatric neck, including abnormalities of the branchial apparatus, thyroglossal duct anomalies, and neoplastic processes, are given. An approach to establishing a differential diagnosis is provided, and critical points of information are summarized. Copyright © 2012 Elsevier Inc. All rights reserved.

[Tall stature: some classical syndromes].

PubMed

Gusbin, N; Verloes, A; Daly, A; Beckers, A

2006-01-01

We describe the findings of XYY syndrome in the setting of encountering an individual with this particular condition in the endocrinology clinic. XYY syndrome is a relatively frequent if unfamiliar condition, which is characterized by taller than average height. The extra Y chromosome may play a role in determining the height of these individuals. From this case, a differential diagnosis of tall stature is outlined, in addition to a description of the principal syndromes associated with gigantism. These primarily include Klinefelter syndrome, Marfan syndrome, androgen resistance and growth hormone excess. These various entities are described from the point of view of their symptomatology, biology, pathophysiology and therapeutic characteristics.

ELECTRON MICROSCOPIC OBSERVATIONS OF AMOEBA PROTEUS IN GROWTH AND INANITION

PubMed Central

Cohen, Adolph I.

1957-01-01

Electron microscopic observations have been made on growing and dividing specimens of Amoeba proteus and also on starving animals. Structures presumably corresponding to the mitochondria, alpha particles, vacuoles, and Golgi material are described. A new entity, designated as a foamy particle, is noted. Descriptions are given of the cytoplasmic and nuclear membranes. During division the inner, thick nuclear membrane component is seen to vanish and the outer membrane persist. Measurements suggest a gradual reappearance of the inner component with growth. Starving animals show a loss of cytoplasmic granularity and an increase in the electron density of mitochondria, presumably due to lipide accumulation. PMID:13481020

Electron microscopic observations of amoeba proteus in growth and inanition.

PubMed

COHEN, A I

1957-11-25

Electron microscopic observations have been made on growing and dividing specimens of Amoeba proteus and also on starving animals. Structures presumably corresponding to the mitochondria, alpha particles, vacuoles, and Golgi material are described. A new entity, designated as a foamy particle, is noted. Descriptions are given of the cytoplasmic and nuclear membranes. During division the inner, thick nuclear membrane component is seen to vanish and the outer membrane persist. Measurements suggest a gradual reappearance of the inner component with growth. Starving animals show a loss of cytoplasmic granularity and an increase in the electron density of mitochondria, presumably due to lipide accumulation.

[WHO classification of head and neck tumours 2017: Main novelties and update of diagnostic methods].

PubMed

Sarradin, Victor; Siegfried, Aurore; Uro-Coste, Emmanuelle; Delord, Jean-Pierre

2018-06-01

The publication of the new WHO classification of head and neck tumours in 2017 brought major modifications. Especially, a new chapter is dedicated to the oropharynx, focusing on the description of squamous cell carcinoma induced by the virus Human Papilloma Virus (HPV), and new entities of tumors are described in nasal cavities and sinuses. In this article are presented the novelties and main changes of this new classification, as well as the updates of the diagnostic methods (immunohistochemistry, cytogenetics or molecular biology). Copyright © 2018 Société Française du Cancer. Published by Elsevier Masson SAS. All rights reserved.

The financial impact of hospitals on the local economy--2 new factors.

PubMed

Rotarius, Timothy; Liberman, Aaron

2014-01-01

This research effort presents a descriptive analysis of the financial impact that several hospitals have on their local economy. An earlier study published by the authors included 3 distinct, yet overlapping components of financial impact: (1) the hospital system as a major health care provider, (2) the hospital system as a large employer, and (3) the hospital system as an entity whose employees contribute greatly to their local community. This new study added additional financial impact factors: (4) the hospital system as an organization committed to major construction projects in pursuit of its health services mission, and (5) the hospital system as an entity that pays taxes to government agencies. The inextricable relationship of these 5 categories both increases and enhances the impact of the hospital system on the local region. The results of this updated and expanded analysis suggest strongly that the hospital system represents 1 of the primary contributors to the economy of the region. The hospital system adds $3 billion to the $28 billion local economy, which means that the hospital system and its employees are responsible for 10.7% of the total economic prowess of the region.

[The nosological entity bulimia nerviosa].

PubMed

López-Ibor Aliño, J J; Cervera Enguix, S

1991-01-01

Anorexia nervosa and bulimia nervosa are at the present moment, two well defined clinical entities among the group of the eating disorders. The psychopathological differentiation of both syndromes has a great importance for diagnosis and therapy. The authors make a phenomenological description, based on case histories of patients with diagnostics of anorexia and bulimia nervosa, and try to establish an approach to the essential symptomatology of those disorders. The presence of affective symptomatology--depressive, but not exclusively--in the eating behaviour disorders in general and particularly in bulimia nervosa, is nowadays interpreted as an unspecific emotional lability as a response to stressing situations. That is to say, it is a secondary depressive symptomatology, more than a primary mood disorder preceding or underlying bulimia. There is strong evidence in favour of a dysregulation of serotonin metabolism in patients with bulimia nervosa, in the sense of a reduced activity, which manifest itself clinically by binges with food with a high content in carbohydrates. High levels of 5-HT seem to induce increasing feelings of safety, fullness and lead to an interruption of eating. Fluoxetine and this active metabolite are selective inhibitors of the reuptake of 5-HT and their antibulimic effect could be mediated by this mechanism.

Contribution of capillary electrophoresis to an integrated vision of humic substances size and charge characterizations

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

D'Orlye, Fanny; Reiller, Pascal E.

2014-02-15

The physicochemical properties of three different humic substances (HS) are probed using capillary zone electrophoresis in alkaline carbonate buffers, pH 10. Special attention is drawn to the impact of the electrolyte ionic strength and counter-ion nature, chosen within the alkali-metal series, on HS electrophoretic mobility. Taylor-Aris dispersion analysis provides insights into the hydrodynamic radius (R-H) distributions of HS. The smallest characterized entities are of nano-metric dimensions, showing neither ionic strength- nor alkali-metal-induced aggregation. These results are compared with the entities evidenced in dynamic light scattering measurements, the size of which is two order of magnitude higher, ca. 100 nm. Themore » extended Onsager model provides a reasonable description of measured electrophoretic mobilities in the ionic strength range 1-50 mM, thus allowing the estimation of limiting mobilities and ionic charge numbers for the different HS samples. An unexpected HS electrophoretic mobility increase (in absolute value) is observed in the order Li{sup +} ≤ Na{sup +} ≤ K{sup +} ≤ Cs{sup +} and discussed either in terms of retarding forces or in terms of ion-ion interactions. (authors)« less

EBV-Positive Lymphoproliferations of B- T- and NK-Cell Derivation in Non-Immunocompromised Hosts

PubMed Central

Fend, Falko

2018-01-01

The contribution of Epstein-Barr virus (EBV) to the development of specific types of benign lymphoproliferations and malignant lymphomas has been extensively studied since the discovery of the virus over the last 50 years. The importance and better understanding of the EBV-associated lymphoproliferative disorders (LPD) of B, T or natural killer (NK) cell type has resulted in the recognition of new entities like EBV+ mucocutaneous ulcer or the addition of chronic active EBV (CAEBV) infection in the revised 2016 World Health Organization (WHO) lymphoma classification. In this article, we review the definitions, morphology, pathogenesis, and evolving concepts of the various EBV-associated disorders including EBV+ diffuse large B-cell lymphoma, not otherwise specified (DLBCL, NOS), EBV+ mucocutaneous ulcer, DLBCL associated with chronic inflammation, fibrin-associated DLBCL, lymphomatoid granulomatosis, the EBV+ T and NK-cell LPD of childhood, aggressive NK leukaemia, extranodal NK/T-cell lymphoma, nasal type, and the new provisional entity of primary EBV+ nodal T- or NK-cell lymphoma. The current knowledge regarding the pathogenesis of B-cell lymphomas that can be EBV-associated including Burkitt lymphoma, plasmablastic lymphoma and classic Hodgkin lymphoma will be also explored. PMID:29518976

Biomine: predicting links between biological entities using network models of heterogeneous databases.

PubMed

Eronen, Lauri; Toivonen, Hannu

2012-06-06

Biological databases contain large amounts of data concerning the functions and associations of genes and proteins. Integration of data from several such databases into a single repository can aid the discovery of previously unknown connections spanning multiple types of relationships and databases. Biomine is a system that integrates cross-references from several biological databases into a graph model with multiple types of edges, such as protein interactions, gene-disease associations and gene ontology annotations. Edges are weighted based on their type, reliability, and informativeness. We present Biomine and evaluate its performance in link prediction, where the goal is to predict pairs of nodes that will be connected in the future, based on current data. In particular, we formulate protein interaction prediction and disease gene prioritization tasks as instances of link prediction. The predictions are based on a proximity measure computed on the integrated graph. We consider and experiment with several such measures, and perform a parameter optimization procedure where different edge types are weighted to optimize link prediction accuracy. We also propose a novel method for disease-gene prioritization, defined as finding a subset of candidate genes that cluster together in the graph. We experimentally evaluate Biomine by predicting future annotations in the source databases and prioritizing lists of putative disease genes. The experimental results show that Biomine has strong potential for predicting links when a set of selected candidate links is available. The predictions obtained using the entire Biomine dataset are shown to clearly outperform ones obtained using any single source of data alone, when different types of links are suitably weighted. In the gene prioritization task, an established reference set of disease-associated genes is useful, but the results show that under favorable conditions, Biomine can also perform well when no such information is available.The Biomine system is a proof of concept. Its current version contains 1.1 million entities and 8.1 million relations between them, with focus on human genetics. Some of its functionalities are available in a public query interface at http://biomine.cs.helsinki.fi, allowing searching for and visualizing connections between given biological entities.

Three Dimensional Shallow Water Adaptive Hydraulics (ADH-SW3): Waterborne Vessels

DTIC Science & Technology

2015-10-01

Type Value Description 1 char CBOW Card type 2 int > 0 Vessel number 3 real # Ratio of vessel bow to vessel draft CSTR FRACTION OF DRAFT...APPLIED TO PSTR Field Type Value Description 1 char CSTR Card type 2 int > 0 Vessel number 3 real # Ratio of vessel stern to vessel draft PROP

75 FR 56013 - Technical Amendments to Pesticide Regulations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-15

...: Kathryn Boyle, Field and External Affairs Division, Office of Pesticide Programs, Environmental Protection... number: (703) 305-5884; e- mail address: boyle.kathryn@epa.gov . SUPPLEMENTARY INFORMATION: I. Does this.... Other types of entities not listed in this unit could also be affected. The North American Industrial...

75 FR 55634 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-13

...: 1505-0209. Type of Review: Revision of a currently approved collection. Title: Troubled Asset Relief Program--Conflicts of Interest. Abstract: The interim rule sets forth the process for reviewing and addressing actual or potential conflicts of interest among any individuals or entities seeking or having a...

Are school children ready to donate blood?

PubMed

Thaver, Danyal Hasan; Masud, Nazish; Ashraf, Mariam

2014-01-01

Voluntary non-remunerated blood donors are considered the best among all different types of blood donors for improving the supply of safe blood. Though safe blood transfusion services have improved in Pakistan, but efforts are still required to optimize blood banks and improve recruitment of voluntary donors, such as senior school/college going students as a source of safe blood. This study looks into the awareness of senior school children concerning blood related issues including blood donation. This cross-sectional descriptive study enrolled 106 senior school students of private schools. Data were collected through self-administered questionnaire. Although 90% of the students considered blood as an important entity for saving lives still 56.8% had never thought of donating blood. Respondents had good knowledge regarding the possible spread of HIV/AIDS, and Hepatitis B and C through unsafe transfusions. Possible hindrances to donating blood included fear of needles, fear of acquiring disease, lack of knowledge regarding where to donate blood and lack of trust on blood banks. More than half of the students believed that blood should be bought from professional blood donors. Senior school going children are not ready to donate blood. Lack of knowledge and prevailing misconceptions regarding blood transfusions need to be addressed and mechanisms to motivate and mobilize youth for becoming voluntary blood donors need to be established.

Epidermal growth factor receptor expression in different subtypes of oral lichenoid disease.

PubMed

Cortés-Ramírez, Dionisio-Alejandro; Rodríguez-Tojo, María-Jose; Coca-Meneses, Juan-Carlos; Marichalar-Mendia, Xabier; Aguirre-Urizar, José-Manuel

2014-09-01

The oral lichenoid disease (OLD) includes different chronic inflammatory processes such as oral lichen planus (OLP) and oral lichenoid lesions (OLL), both entities with controversial diagnosis and malignant potential. Epidermal growth factor receptor (EFGR) is an important oral carcinogenesis biomarker and overexpressed in several oral potentially malignant disorders. To analyze the EGFR expression in the OLD to find differences between OLP and OLL, and to correlate it with the main clinical and pathological features. Forty-four OLD cases were studied and classified according to their clinical (Group C1: only papular lesions / Group C2: papular and other lesions) and histopathological features (Group HT: OLP-typical / Group HC: OLP-compatible) based in previous published criteria. Standard immunohistochemical identification of EGFR protein was performed. Comparative and descriptive statistical analyses were performed. Thirty-five cases (79.5%) showed EGFR overexpression without significant differences between clinical and histopathological groups (p<0.05). Histological groups showed significant differences in the EGFR expression pattern (p=0.016). Conlusions: All OLD samples showed high EGFR expression. The type of clinical lesion was not related with EGFR expression; however, there are differences in the EGFR expression pattern between histological groups that may be related with a different biological profile and malignant risk.

No longer a circumtropical species: revision of the lizardfishes in the Trachinocephalus myops species complex, with description of a new species from the Marquesas Islands.

PubMed

Polanco F, A; Acero P, A; Betancur-R, R

2016-08-01

Trachinocephalus, a formerly monotypic and nearly circumtropical genus of lizardfishes, is split into three valid species. Trachinocephalus gauguini n. sp. is described from the Marquesas Islands and is distinguished from the two other species in the genus by having a shorter snout, a narrower interorbital space, larger eye and modally fewer anal-fin and pectoral-fin rays. The distribution of Trachinocephalus myops (type species) is restricted to the Atlantic Ocean and the name Trachinocephalus trachinus is resurrected for populations from the Indo-West Pacific Ocean. Principal component analyses and bivariate plots based on the morphometric data differentiated T. gauguini from the other two species, but a substantial overlap between T. myops and T. trachinus exists. Phylogenetic evidence based on mtDNA COI sequences unambiguously supports the recognition of at least three species in Trachinocephalus, revealing deep divergences between the Atlantic Ocean, Indo-West Pacific Ocean and Marquesas entities. Additional analyses of species delimitations using the generalized mixed Yule coalescent model and the Poisson tree processes model provide a more liberal assessment of species in Trachinocephalus, indicating that many more cryptic species may exist. Finally, a taxonomic key to identify the three species recognized here is provided. © 2016 The Fisheries Society of the British Isles.

Integrating publicly-available data to generate computationally ...

EPA Pesticide Factsheets

The adverse outcome pathway (AOP) framework provides a way of organizing knowledge related to the key biological events that result in a particular health outcome. For the majority of environmental chemicals, the availability of curated pathways characterizing potential toxicity is limited. Methods are needed to assimilate large amounts of available molecular data and quickly generate putative AOPs for further testing and use in hazard assessment. A graph-based workflow was used to facilitate the integration of multiple data types to generate computationally-predicted (cp) AOPs. Edges between graph entities were identified through direct experimental or literature information or computationally inferred using frequent itemset mining. Data from the TG-GATEs and ToxCast programs were used to channel large-scale toxicogenomics information into a cpAOP network (cpAOPnet) of over 20,000 relationships describing connections between chemical treatments, phenotypes, and perturbed pathways measured by differential gene expression and high-throughput screening targets. Sub-networks of cpAOPs for a reference chemical (carbon tetrachloride, CCl4) and outcome (hepatic steatosis) were extracted using the network topology. Comparison of the cpAOP subnetworks to published mechanistic descriptions for both CCl4 toxicity and hepatic steatosis demonstrate that computational approaches can be used to replicate manually curated AOPs and identify pathway targets that lack genomic mar

[A family with progressive myoclonus epilepsy (author's transl)].

PubMed

Ammann, F; Schweingruber, R; Paro, M

1978-01-01

To begin, a survey of the literature concerning the group of progressive myoclonic epilepsies is presented, from the initial descriptions of Unverricht (1891) and Lundborg (1903) to the present. Recently several subforms of this nosologic entity have been delineated according to the mode of inheritance, time of manifestation, severity of course, and biochemical characteristics (i.e, eventual demonstration of mucopolysaccharide storage in Lafora bodies or diffuse in the central nervous system and other organs). The most useful classification stems from Diebold (1972): early (I) and late (II) forms of the Lafora type having autosomal recessive inheritance; an autosomal recessive early form (III) and an autosomal dominant late form (IV) with degenerative changes in the central nervous system without biochemical disturbances. The authors describe 3 young siblings from Southern Tyrol, who clinically manifested the cardinal symptoms of the disease in addition to extrapyramidal cerebellar disturbances. In spite of extensive bioptic and biochemical examinations, neither Lafora bodies nor diffuse deposits or excretion of mucopolysaccharides could be demonstrated. The distant blood relationship between the parents of these patients supports the assumption of an autosomal recessive mode of transmission. The relatively early manifestation of the disease and the demonstration of degenerative changes within the central nervous system suggest assignment of these patients to Diebold's subgroup III of the progressive myoclonic epilepsy.

Type II toxin: antitoxin systems. More than small selfish entities?

PubMed

Rocker, Andrea; Meinhart, Anton

2016-05-01

Toxin-antitoxin (TA) modules regulate metabolism and viability of bacteria and archaea. In type II TA systems these functions are generally thought to be performed by two small proteins. However, evidence is increasing that the toxins are much more diverse and can form multi-domain proteins. Recently, we published a novel type II TA system in which toxin and antitoxin are covalently linked into a single polypeptide chain. In this review we summarize the current knowledge on these elongated toxin homologs and provide perspectives for future study.

Implementation of a frame-based representation in CLIPS

NASA Technical Reports Server (NTRS)

Assal, Hisham; Myers, Leonard

1990-01-01

Knowledge representation is one of the major concerns in expert systems. The representation of domain-specific knowledge should agree with the nature of the domain entities and their use in the real world. For example, architectural applications deal with objects and entities such as spaces, walls, and windows. A natural way of representing these architectural entities is provided by frames. This research explores the potential of using the expert system shell CLIPS, developed by NASA, to implement a frame-based representation that can accommodate architectural knowledge. These frames are similar but quite different from the 'template' construct in version 4.3 of CLIPS. Templates support only the grouping of related information and the assignment of default values to template fields. In addition to these features frames provide other capabilities including definition of classes, inheritance between classes and subclasses, relation of objects of different classes with 'has-a', association of methods (demons) of different types (standard and user-defined) to fields (slots), and creation of new fields at run-time. This frame-based representation is implemented completely in CLIPS. No change to the source code is necessary.

Emerald: an object-based language for distributed programming

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

Hutchinson, N.C.

1987-01-01

Distributed systems have become more common, however constructing distributed applications remains a very difficult task. Numerous operating systems and programming languages have been proposed that attempt to simplify the programming of distributed applications. Here a programing language called Emerald is presented that simplifies distributed programming by extending the concepts of object-based languages to the distributed environment. Emerald supports a single model of computation: the object. Emerald objects include private entities such as integers and Booleans, as well as shared, distributed entities such as compilers, directories, and entire file systems. Emerald objects may move between machines in the system, but objectmore » invocation is location independent. The uniform semantic model used for describing all Emerald objects makes the construction of distributed applications in Emerald much simpler than in systems where the differences in implementation between local and remote entities are visible in the language semantics. Emerald incorporates a type system that deals only with the specification of objects - ignoring differences in implementation. Thus, two different implementations of the same abstraction may be freely mixed.« less

Pustular psoriasis: pathophysiology and current treatment perspectives

PubMed Central

Benjegerdes, Katie E; Hyde, Kimberly; Kivelevitch, Dario; Mansouri, Bobbak

2016-01-01

Psoriasis vulgaris is a chronic inflammatory disease that classically affects skin and joints and is associated with numerous comorbidities. There are several clinical subtypes of psoriasis including the uncommon pustular variants, which are subdivided into generalized and localized forms. Generalized forms of pustular psoriasis include acute generalized pustular psoriasis, pustular psoriasis of pregnancy, and infantile and juvenile pustular psoriasis. Localized forms include acrodermatitis continua of Hallopeau and palmoplantar pustular psoriasis. These subtypes vary in their presentations, but all have similar histopathologic characteristics. The immunopathogenesis of each entity remains to be fully elucidated and some debate exists as to whether these inflammatory pustular dermatoses should be classified as entities distinct from psoriasis vulgaris. Due to the rarity of these conditions and the questionable link to the common, plaque-type psoriasis, numerous therapies have shown variable results and most entities remain difficult to treat. With increasing knowledge of the pathogenesis of these variants of pustular psoriasis, the development and use of biologic and other immunomodulatory therapies holds promise for the future of successfully treating pustular variants of psoriasis. PMID:29387600

Printable, scannable biometric templates for secure documents and materials

NASA Astrophysics Data System (ADS)

Cambier, James L.; Musgrave, Clyde

2000-04-01

Biometric technology has been widely acknowledged as an effective means for enhancing private and public security through applications in physical access control, computer and computer network access control, medical records protection, banking security, public identification programs, and others. Nearly all of these applications involve use of a biometric token to control access to a physical entity or private information. There are also unique benefits to be derived from attaching a biometric template to a physical entity such as a document, package, laboratory sample, etc. Such an association allows fast, reliable, and highly accurate association of an individual person's identity to the physical entity, and can be used to enhance security, convenience, and privacy in many types of transactions. Examples include authentication of documents, tracking of laboratory samples in a testing environment, monitoring the movement of physical evidence within the criminal justice system, and authenticating the identity of both sending and receiving parties in shipment of high value parcels. A system is described which combines a biometric technology based on iris recognition with a printing and scanning technology for high-density bar codes.

The definitions of information and meaning two possible boundaries between physics and biology.

PubMed

Barbieri, Marcello

2004-01-01

The standard approach to the definition of the physical quantities has not produced satisfactory results with the concepts of information and meaning. In the case of information we have at least two unrelated definitions, while in the case of meaning we have no definition at all. Here it is shown that both information and meaning can be defined by operative procedures, but it is also pointed out that we need to recognize them as a new type of natural entities. They are not quantities (neither fundamental nor derived) because they cannot be measured, and they are not qualities because are not subjective features. Here it is proposed to call them nominable entities, i.e., entities which can be specified only by naming their components in their natural order. If the genetic code is not a linguistic metaphor but a reality, we must conclude that information and meaning are real natural entities, and now we must also conclude that they are not equivalent to the quantities and qualities of our present theoretical framework. This gives us two options. One is to extend the definition of physics and say that the list of its fundamental entities must include information and meaning. The other is to say that physics is the science of quantities only, and in this case information and meaning become the exclusive province of biology. The boundary between physics and biology, in short, is a matter of convention, but the existence of information and meaning is not. We can decide to study them in the framework of an extended physics or in a purely biological framework, but we cannot avoid studying them for what they are, i.e., as fundamental components of the fabric of Nature.

Characterization of Departures from Regulatory Requirements Identified During Inspections Conducted by the US Federal Select Agent Program, 2014-15.

PubMed

Bjork, Adam; Sosin, Daniel M

We studied departures from regulatory requirements identified on US Federal Select Agent Program (FSAP) inspections to increase transparency regarding biosafety and security risk at FSAP-regulated entities and identify areas for programmatic improvement. Regulatory departures from inspections led by Centers for Disease Control and Prevention inspectors during 2014-15 were grouped into "biosafety," "security," and "other" observation categories and assigned a risk level and score reflecting perceived severity. The resulting 2,267 biosafety (n = 1,153) and security (n = 1,114) observations from 296 inspections were analyzed by frequency and risk across entity and inspection characteristics. The greatest proportion of biosafety observations involved equipment and facilities (28%), and the greatest proportion of security observations involved access restrictions (33%). The greatest proportion of higher-risk observations for biosafety were containment issues and for security were inventory discrepancies. Commercial entities had the highest median cumulative risk score per inspection (17), followed by private (13), academic (10), federal government (10), and nonfederal government (8). Maximum containment (BSL-4) inspections had higher median biosafety risk per inspection (13) than other inspections (5) and lower security risk (0 vs 4). Unannounced inspections had proportionally more upper risk level observations than announced (biosafety, 21% vs 12%; security, 18% vs 7%). Possessors of select agents had higher median biosafety risk per inspection (6) than nonpossessors (4) and more upper risk level security observations (10% vs 0%). Programmatic changes to balance resources according to entity risk may strengthen FSAP oversight. Varying inspection methods by select agent possession and entity type, and conducting more unannounced inspections, may be beneficial.

13 CFR 130.200 - Eligible entities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 13 Business Credit and Assistance 1 2011-01-01 2011-01-01 false Eligible entities. 130.200 Section... CENTERS § 130.200 Eligible entities. (a) Recipient Organization. The following entities are eligible to... community or junior college; (5) An entity formed by two or more of the above entities; or (6) Any entity...

78 FR 77126 - Information Collection Being Submitted for Review and Approval to the Office of Management and...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-20

... currently approved collection. Respondents: Businesses or other for-profit entities; Individuals or... information technology; and ways to further reduce the information collection burden on small business... Form 160. Type of Review: Extension of a currently approved collection. Respondents: Businesses or...

32 CFR 32.27 - Allowable costs.

Code of Federal Regulations, 2010 CFR

2010-07-01

... contractor receiving a. cost-type contract under an assistance award, there is a set of Federal principles... principles applicable to the entity incurring the costs. (b) Governmental organizations. Allowability of... of OMB Circular A-87, 8 “Cost Principles for State and Local Governments.” 8 See footnote 1 to § 32.1...

76 FR 4094 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2011-01-24

...). Title: Trademark Trial and Appeal Board (TTAB) Actions. Form Number(s): PTO 2120, 2151, 2153, and 2188 through 2190. Agency Approval Number: 0651-0040. Type of Request: Revision of a currently approved... a petition to cancel the registration of that mark. Individuals or entities may file an appeal from...

78 FR 32251 - Information Collection Being Reviewed by the Federal Communications Commission Under Delegated...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-29

... opportunity to comment on the following information collection, as required by the Paperwork Reduction Act.... Type of Review: Extension of a currently approved collection. Respondents: Business or other for-profit entities, Not-for-profit institutions. Number of Respondents and Responses: 300 respondents; 300 responses...

19 CFR 191.193 - Application procedure for compliance program.

Code of Federal Regulations, 2010 CFR

2010-04-01

... participation in the drawback compliance program. This includes any person, corporation or business entity that... part). The detail required in the application shall take into account the size and nature of the applicant's drawback program, the type of drawback claims filed, and the dollar value and volume of claims...

10 CFR 600.501 - Definitions.

Code of Federal Regulations, 2010 CFR

2010-01-01

.... Company means any business entity other than an organization of the type described in section 501(c)(3) of... maintained and published by the Department of Energy.) Parent company means a company that: (1) Exercises ultimate ownership of the applicant company either directly, by ownership of a majority of that company's...

78 FR 57371 - Agency Information Collection Activities; Comment Request; Student Aid Internet Gateway (SAIG...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-18

...; Comment Request; Student Aid Internet Gateway (SAIG) Enrollment Document AGENCY: Federal Student Aid (FSA... Internet Gateway (SAIG) Enrollment Document. OMB Control Number: 1845-0002. Type of Review: A revision of... Internet Gateway (SAIG) allows eligible entities to securely exchange Title IV, Higher Education Act (HEA...

17 CFR 165.9 - Criteria for determining amount of award.

Code of Federal Regulations, 2013 CFR

2013-04-01

...; (v) The efforts undertaken by the whistleblower to remediate the harm caused by the violations of the... reduced or eliminated by the Commission because an entity self-reported a commodities violation following... harm or potential harm caused by the underlying violations, the type of harm resulting from or...

17 CFR 165.9 - Criteria for determining amount of award.

Code of Federal Regulations, 2014 CFR

2014-04-01

... the harm caused by the violations of the Commodity Exchange Act, including assisting the authorities... potential monetary sanctions were reduced or eliminated by the Commission because an entity self-reported a... amount of harm or potential harm caused by the underlying violations, the type of harm resulting from or...

17 CFR 165.9 - Criteria for determining amount of award.

Code of Federal Regulations, 2012 CFR

2012-04-01

...; (v) The efforts undertaken by the whistleblower to remediate the harm caused by the violations of the... reduced or eliminated by the Commission because an entity self-reported a commodities violation following... harm or potential harm caused by the underlying violations, the type of harm resulting from or...

Restorer-of-fertility mutations recovered in transposon-active lines of S male-sterile maize

USDA-ARS?s Scientific Manuscript database

Mitochondria execute key pathways of central metabolism and serve as cellular sensing and signaling entities - functions that depend upon interactions between mitochondrial and nuclear genetic systems. This is exemplified in cytoplasmic male sterility type S (CMS-S) of Zea mays, where novel mitochon...

Bank Community Development Corporations.

ERIC Educational Resources Information Center

Illinois State Dept. of Commerce and Community Affairs, Springfield.

This handbook provides a brief overview of bank and bank holding company community development corporations (CDCs), the types of activities for which they can be used, the legal requirements in establishing such an entity, and how they are organized and operated. Case studies, including studies of the Shorebank Corporation of Chicago, the First…

Modeling Of Object- And Scene-Prototypes With Hierarchically Structured Classes

NASA Astrophysics Data System (ADS)

Ren, Z.; Jensch, P.; Ameling, W.

1989-03-01

The success of knowledge-based image analysis methodology and implementation tools depends largely on an appropriately and efficiently built model wherein the domain-specific context information about and the inherent structure of the observed image scene have been encoded. For identifying an object in an application environment a computer vision system needs to know firstly the description of the object to be found in an image or in an image sequence, secondly the corresponding relationships between object descriptions within the image sequence. This paper presents models of image objects scenes by means of hierarchically structured classes. Using the topovisual formalism of graph and higraph, we are currently studying principally the relational aspect and data abstraction of the modeling in order to visualize the structural nature resident in image objects and scenes, and to formalize. their descriptions. The goal is to expose the structure of image scene and the correspondence of image objects in the low level image interpretation. process. The object-based system design approach has been applied to build the model base. We utilize the object-oriented programming language C + + for designing, testing and implementing the abstracted entity classes and the operation structures which have been modeled topovisually. The reference images used for modeling prototypes of objects and scenes are from industrial environments as'well as medical applications.

Antarctic Meteorite Newsletter, volume 9, no. 2

NASA Technical Reports Server (NTRS)

Gooding, J. L. (Editor)

1986-01-01

Preliminary description and classifications of meteorites that were completed since publication of the February issue are contained. Most large (greater than 150 g) specimens (regardless of petrologic type) and all pebble sized (less than 150 g) specimens of special petrologic type are represented by separate descriptions. However, specimens of nonspecial petrologic type are listed only as single line entries. For convenience, new specimens are also recast by petrologic type. Each macroscopic description summarizes features that were visible to the eye at the time the meteorite was first examined. Classification is based on microscopic petrography and resonnaissance-level electron-probe microanalysis. The pairing list was updated.

Flavor lexicon for sensory descriptive profiling of different rice types.

PubMed

Limpawattana, M; Shewfelt, R L

2010-05-01

Rice flavor is a significant factor in determining quality and consumer acceptability as exemplified by scented rice, which is highly favored and commands a price premium. Sensory descriptive analysis has primarily been performed to assess rice flavor characteristics, but these studies feature only a limited lexicon for characterizing specific flavors or the range of flavor types is limited. This study was undertaken to establish a descriptive lexicon with reference standards for describing the flavor properties of a broad spectrum of rice types and use the developed lexicon to characterize which sensory attributes are most important in rice flavor quality. A rice flavor lexicon consisting of 24 descriptive notes was developed and expanded by 8 trained sensory panelists to characterize the flavor of cooked rice differing in terms of forms, types, and specialty (n = 36). Of these 24 descriptive terms, 19 were aromatic notes and 5 were fundamental tastes and oral feeling factors. Eighteen aromatic terms were significantly present in most rice samples whereas some descriptors exhibited unique characteristics of a specific-rice type. Subsequent multivariate analysis indicated that 18 descriptive terms were required to fully understand the characteristics of rice flavor in greater details. This lexicon covered a wider range of rice samples than in the previous studies and will facilitate targeting the characteristic notes important to rice processors as well as producers.

The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs

PubMed Central

Bard, Jonathan B. L.

2012-01-01

This paper describes the AEO, an ontology of anatomical entities that expands the common anatomy reference ontology (CARO) and whose major novel feature is a type hierarchy of ~160 anatomical terms. The breadth of the AEO is wider than CARO as it includes both developmental and gender-specific classes, while the granularity of the AEO terms is at a level adequate to classify simple-tissues (~70 classes) characterized by their containing a predominantly single cell-type. For convenience and to facilitate interoperability, the AEO contains an abbreviated version of the ontology of cell-types (~100 classes) that is linked to these simple-tissue types. The AEO was initially based on an analysis of a broad range of animal anatomy ontologies and then upgraded as it was used to classify the ~2500 concepts in a new version of the ontology of human developmental anatomy (www.obofoundry.org/), a process that led to significant improvements in its structure and content, albeit with a possible focus on mammalian embryos. The AEO is intended to provide the formal classification expected in contemporary ontologies as well as capturing knowledge about anatomical structures not currently included in anatomical ontologies. The AEO may thus be useful in increasing the amount of tissue and cell-type knowledge in other anatomy ontologies, facilitating annotation of tissues that share common features, and enabling interoperability across anatomy ontologies. The AEO can be downloaded from http://www.obofoundry.org/. PMID:22347883

Spine malformation complex in 3 diverse syndromic entities: Case reports.

PubMed

Kaissi, Ali Al; van Egmond-Fröhlich, Andreas; Ryabykh, Sergey; Ochirov, Polina; Kenis, Vladimir; Hofstaetter, Jochen G; Grill, Franz; Ganger, Rudolf; Kircher, Susanne Gerit

2016-12-01

Clinical and radiographic phenotypic characterizations were the base line tool of diagnosis in 3 syndromic disorders in which congenital cervico-thoracic kyphosis was the major deformity. Directing maximal care toward the radiographic analysis is not only the axial malformation but also toward the appendicular abnormalities was our main concern. We fully documented the diversity of the spine phenotypic malformation complex via the clinical and radiographic phenotypes. We established the diagnosis via phenotypic/genotypic confirmation in 3 diverse syndromic entities namely acampomelic campomelic dysplasia, Larsen syndrome and Morquio syndrome type A (mucopolysaccharidosis type IV A). Surgical interventions have been carried out in the Larsen syndrome and Morquio syndrome type A, resepectively. The earliest the diagnosis is, the better the results are. The necessity to diagnose children in their first year of life has many folds, firstly the management would be in favor of the child's growth and development and secondly, the prognosis could be clearer to the family and the medical staff as well. Our current paper is to sensitize paediatricians, physicians and orthopedic surgeons regarding the necessity to detect the aetiological understanding in every child who manifests a constellation of malformation complex. Scoliosis and kyphosis/kyphoscoliosis are not a diagnosis in themselves. Such deformities are mostly a symptom complex correlated to dozens of types of syndromic associations. The rate curve progression and the final severity of congenital spine tilting are related to 3 factors: (a) the type of vertebral malformation present, (b) the patient's phenotype, and (c) the diagnosis.

The AEO, an Ontology of Anatomical Entities for Classifying Animal Tissues and Organs.

PubMed

Bard, Jonathan B L

2012-01-01

This paper describes the AEO, an ontology of anatomical entities that expands the common anatomy reference ontology (CARO) and whose major novel feature is a type hierarchy of ~160 anatomical terms. The breadth of the AEO is wider than CARO as it includes both developmental and gender-specific classes, while the granularity of the AEO terms is at a level adequate to classify simple-tissues (~70 classes) characterized by their containing a predominantly single cell-type. For convenience and to facilitate interoperability, the AEO contains an abbreviated version of the ontology of cell-types (~100 classes) that is linked to these simple-tissue types. The AEO was initially based on an analysis of a broad range of animal anatomy ontologies and then upgraded as it was used to classify the ~2500 concepts in a new version of the ontology of human developmental anatomy (www.obofoundry.org/), a process that led to significant improvements in its structure and content, albeit with a possible focus on mammalian embryos. The AEO is intended to provide the formal classification expected in contemporary ontologies as well as capturing knowledge about anatomical structures not currently included in anatomical ontologies. The AEO may thus be useful in increasing the amount of tissue and cell-type knowledge in other anatomy ontologies, facilitating annotation of tissues that share common features, and enabling interoperability across anatomy ontologies. The AEO can be downloaded from http://www.obofoundry.org/.

Assessment of disease named entity recognition on a corpus of annotated sentences.

PubMed

Jimeno, Antonio; Jimenez-Ruiz, Ernesto; Lee, Vivian; Gaudan, Sylvain; Berlanga, Rafael; Rebholz-Schuhmann, Dietrich

2008-04-11

In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other semantic types like diseases have not received the same level of attention. Different solutions have been proposed to identify disease named entities in the scientific literature. While matching the terminology with language patterns suffers from low recall (e.g., Whatizit) other solutions make use of morpho-syntactic features to better cover the full scope of terminological variability (e.g., MetaMap). Currently, MetaMap that is provided from the National Library of Medicine (NLM) is the state of the art solution for the annotation of concepts from UMLS (Unified Medical Language System) in the literature. Nonetheless, its performance has not yet been assessed on an annotated corpus. In addition, little effort has been invested so far to generate an annotated dataset that links disease entities in text to disease entries in a database, thesaurus or ontology and that could serve as a gold standard to benchmark text mining solutions. As part of our research work, we have taken a corpus that has been delivered in the past for the identification of associations of genes to diseases based on the UMLS Metathesaurus and we have reprocessed and re-annotated the corpus. We have gathered annotations for disease entities from two curators, analyzed their disagreement (0.51 in the kappa-statistic) and composed a single annotated corpus for public use. Thereafter, three solutions for disease named entity recognition including MetaMap have been applied to the corpus to automatically annotate it with UMLS Metathesaurus concepts. The resulting annotations have been benchmarked to compare their performance. The annotated corpus is publicly available at ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases and can serve as a benchmark to other systems. In addition, we found that dictionary look-up already provides competitive results indicating that the use of disease terminology is highly standardized throughout the terminologies and the literature. MetaMap generates precise results at the expense of insufficient recall while our statistical method obtains better recall at a lower precision rate. Even better results in terms of precision are achieved by combining at least two of the three methods leading, but this approach again lowers recall. Altogether, our analysis gives a better understanding of the complexity of disease annotations in the literature. MetaMap and the dictionary based approach are available through the Whatizit web service infrastructure (Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A: Text processing through Web services: Calling Whatizit. Bioinformatics 2008, 24:296-298).

Classification and description of world formation types. Part II (Description of formation types)

Treesearch

D. Faber-Langendoen; T. Keeler-Wolf; D. Meidinger; C. Josse; A. Weakley; D. Tart; G. Navarro; B. Hoagland; S. Ponomarenko; J.P. Saucier; G. Fults; E. Helmer

2012-01-01

A vegetation-ecologic classification approach has been developed in which a combination of vegetation attributes (physiognomy, structure, and floristics) and their response to ecological and biogeographic factors are used as the basis for classifying vegetation types (Faber-Langendoen et al. 2012). This approach can help support international, national and subnational...

Level of Awareness and Knowledge of Breast Cancer in Nigeria. A Systematic Review.

PubMed

Olayide, Agodirin S; Halimat, Akande J; Samuel, Olatoke A; Ganiyu, Rahman A; Soliu, Oguntola A

2017-03-01

Despite reports of improved awareness of breast cancer entity and seemingly upbeat levels of other awareness subthemes in Nigeria, patients continue to present late when treatment is least rewarding. This paradoxical trend of both rising awareness and late presentation coupled with reports suggesting other competing drivers of late presentation question the "theory of poor awareness" as the foremost driver of late presentations. By aggregating available data, we aimed to assess what still constitutes poor breast cancer awareness in Nigeria in order to suggest how to allocate resources to reverse the paradox. Studies conducted on Nigerian populace from 2000 to date were reviewed systematically. Search was made in PROSPERO, PubMed/MEDLINE, AJOL, Cochrane library, GOOGLE, ResearchGate and ACADEMIA. Primary outcome was level of awareness about breast cancer entity. Fifty-one eligible (48 descriptive surveys, 3 interventional ones) studies were reviewed. They included 19,598 respondents (98.5% females; 43% rural dwellers). 17,086(87.2%) were laypersons in various walks of life; 2,512(12.8%) were healthcare professionals. There were high levels of awareness of breast cancer entity, BSE, knowledge of fatality and benefit of early detection (weighted percentages 80.6%, 60.1%, 73.2% and 73.9% respectively). Weighted percentages of knowledge of symptoms/signs was 45.1%. Weighted percentages of sense of susceptibility and performance of BSE were low-26.8% and 22.9% respectively. Generally, rate of performance of screening did not vary with changes in the level of awareness/knowledge of concepts. In general, low awareness of breast cancer may not be the direct and foremost driver of persistent late presentation in Nigeria.

Addressing complexity in population health intervention research: the context/intervention interface.

PubMed

Minary, Laetitia; Alla, François; Cambon, Linda; Kivits, Joelle; Potvin, Louise

2018-04-01

Public health interventions are increasingly being recognised as complex and context dependent. Related to this is the need for a systemic and dynamic conception of interventions that raises the question of delineating the scope and contours of interventions in complex systems. This means identifying which elements belong to the intervention (and therefore participate in its effects and can be transferred), which ones belong to the context and interact with the former to influence results (and therefore must be taken into account when transferring the intervention) and which contextual elements are irrelevant to the intervention. This paper, from which derives criteria based on a network framework, operationalises how the context and intervention systems interact and identify what needs to be replicated as interventions are implemented in different contexts. Representing interventions as networks (composed of human and non-human entities), we introduce the idea that the density of interconnections among the various entities provides a criterion for distinguishing core intervention from intervention context without disconnecting the two systems. This differentiates endogenous and exogenous intervention contexts and the mediators that connect them, which form the fuzzy and constantly changing intervention/context interface. We propose that a network framework representing intervention/context systems constitutes a promising approach for deriving empirical criteria to delineate the scope and contour of what is replicable in an intervention. This approach should allow better identification and description of the entities that have to be transferred to ensure the potential effectiveness of an intervention in a specific context. © 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.

Nanomaterials in the Context of Type 2 Immune Responses—Fears and Potentials

PubMed Central

Himly, Martin; Mills-Goodlet, Robert; Geppert, Mark; Duschl, Albert

2017-01-01

The type 2 immune response is an adaptive immune program involved in defense against parasites, detoxification, and wound healing, but is predominantly known for its pathophysiological effects, manifesting as allergic disease. Engineered nanoparticles (NPs) are non-self entities that, to our knowledge, do not stimulate detrimental type 2 responses directly, but have the potential to modulate ongoing reactions in various ways, including the delivery of substances aiming at providing a therapeutic benefit. We review, here, the state of knowledge concerning the interaction of NPs with type 2 immune responses and highlight their potential as a multifunctional platform for therapeutic intervention. PMID:28487697

75 FR 48625 - Amendment to the International Traffic in Arms Regulations: Dual Nationals and Third-Country...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-08-11

..., including technical data, within a foreign business entity, foreign governmental entity, or international..., directly employed by the foreign business entity, foreign governmental entity, or international... any defense article, any foreign business entity, foreign governmental entity, or international...

49 CFR Appendix A to Part 221 - Procedures for Approval of Rear End Marking Devices

Code of Federal Regulations, 2011 CFR

2011-10-01

... description of the device including the type, luminance description, size of lens, manufacturer and catalog number, lamp manufacturer, lamp type and model number, and any auxiliary optics used. (2) A certification...

49 CFR Appendix A to Part 221 - Procedures for Approval of Rear End Marking Devices

Code of Federal Regulations, 2010 CFR

2010-10-01

... description of the device including the type, luminance description, size of lens, manufacturer and catalog number, lamp manufacturer, lamp type and model number, and any auxiliary optics used. (2) A certification...

Dialog detection in narrative video by shot and face analysis

NASA Astrophysics Data System (ADS)

Kroon, B.; Nesvadba, J.; Hanjalic, A.

2007-01-01

The proliferation of captured personal and broadcast content in personal consumer archives necessitates comfortable access to stored audiovisual content. Intuitive retrieval and navigation solutions require however a semantic level that cannot be reached by generic multimedia content analysis alone. A fusion with film grammar rules can help to boost the reliability significantly. The current paper describes the fusion of low-level content analysis cues including face parameters and inter-shot similarities to segment commercial content into film grammar rule-based entities and subsequently classify those sequences into so-called shot reverse shots, i.e. dialog sequences. Moreover shot reverse shot specific mid-level cues are analyzed augmenting the shot reverse shot information with dialog specific descriptions.

Bullous Complex Regional Pain Syndrome: A description of the clinical and histopathologic features.

PubMed

Ho, J D; Al-Haseni; Smith, S; Bhawan, J; Sahni, D

2018-04-27

Complex regional pain syndrome (CRPS, formerly reflex sympathetic dystrophy) is a poorly understood syndrome occurring most commonly after peripheral trauma.(1) Diagnostic features include pain, autonomic dysregulation, sensory/motor abnormalities and trophic changes involving the affected limb.(1,2) Dermatologic findings include erythema, atrophy, xerosis, erosive disease, and reticulated erythematous patches.(3,4) Exceptionally, blistering has been reported.(5-7) Given its rarity, the clinical and histopathologic findings of bullous CRPS are not well described. We report a case of bullous CRPS in a patient with mycosis fungoides (MF), describing the clinical and histopathologic features of this uncommon entity. This article is protected by copyright. All rights reserved.

Hypothyroidism-induced myocardial damage and heart failure: an overlooked entity.

PubMed

Shuvy, Mony; Shifman, Oshrat E Tayer; Nusair, Samir; Pappo, Orit; Lotan, Chaim

2009-01-01

Hypothyroid state may induce cardiac muscle impairment such as diastolic dysfunction and abnormal relaxation time. Advanced heart failure in hypothyroid patients has been described only in severe symptomatic cases, mostly during myxedematous coma. We describe an unusual case of asymptomatic patient with hypothyroidism who presented with severely reduced cardiac function with elevated cardiac enzymes reflecting significant myocardial injury. Comprehensive evaluation for heart failure was suggestive only for long-standing untreated hypothyroidism. Endomyocadial biopsy demonstrated unique histological findings of mucopolysaccharide accumulation attributed to hypothyroid state. Asymptomatic hypothyroidism may cause severe reduction in cardiac function accompanied with elevated cardiac enzymes. To our knowledge, this is the first description of human myocardial biopsy revealing mucopolysaccharide accumulation attributed to hypothyroid state.

ForistomApp a Web application for scientific and technological information management of Forsitom foundation

NASA Astrophysics Data System (ADS)

Saavedra-Duarte, L. A.; Angarita-Jerardino, A.; Ruiz, P. A.; Dulce-Moreno, H. J.; Vera-Rivera, F. H.; V-Niño, E. D.

2017-12-01

Information and Communication Technologies (ICT) are essential in the transfer of knowledge, and the Web tools, as part of ICT, are important for institutions seeking greater visibility of the products developed by their researchers. For this reason, we implemented an application that allows the information management of the FORISTOM Foundation (Foundation of Researchers in Science and Technology of Materials). The application shows a detailed description, not only of all its members also of all the scientific production that they carry out, such as technological developments, research projects, articles, presentations, among others. This application can be implemented by other entities committed to the scientific dissemination and transfer of technology and knowledge.

Breathlessness and blood: a combustible combination.

PubMed

Popovsky, Mark A

2002-08-01

Pulmonary complications are increasingly recognized as serous hazards of transfusion. The evidence suggests that transfusion-related acute lung injury (TRALI) and transfusion-associated circulatory overload (TACO) are underrecognized. Both present with dyspnea but other signs and symptoms assist in determining the proper diagnosis. Males and females are equally affected. Morbidity is significant with both complications and in the case of TRALI, the mortality is in the range of 6-10%. Although the clinical descriptions of both entities are well established, the clinical profile of the at-risk population for both TRALI and TACO is not well understood. Because early intervention can reduce morbidity, it is important that clinicians recognize these disorders and apply appropriate treatment.

AIDS, religious enthusiasm and spiritual insecurity in Africa.

PubMed

Ashforth, Adam

2011-01-01

The connection between the AIDS epidemic and the efflorescence of religious 'enthusiasm' (construed in both classical and contemporary senses) in Africa in recent decades is best understood, this paper argues, by reference to a concept of 'spiritual insecurity'. The article offers a general description of the condition of spiritual insecurity and argues that it is best studied within a relational realist paradigm. The article presents a critique of the concept of 'belief' as commonly used in the social science of religion, arguing instead for an opening of the study of social relations to include the universe of relations within which people experience the world, including their relations with entities such as spiritual beings that might otherwise be considered virtual.

Anticancer drug discovery and pharmaceutical chemistry: a history.

PubMed

Braña, Miguel F; Sánchez-Migallón, Ana

2006-10-01

There are several procedures for the chemical discovery and design of new drugs from the point of view of the pharmaceutical or medicinal chemistry. They range from classical methods to the very new ones, such as molecular modeling or high throughput screening. In this review, we will consider some historical approaches based on the screening of natural products, the chances for luck, the systematic screening of new chemical entities and serendipity. Another group comprises rational design, as in the case of metabolic pathways, conformation versus configuration and, finally, a brief description on available new targets to be carried out. In each approach, the structure of some examples of clinical interest will be shown.

Describing the silent human virome with an emphasis on giant viruses.

PubMed

Popgeorgiev, Nikolay; Temmam, Sarah; Raoult, Didier; Desnues, Christelle

2013-01-01

Viruses are the most abundant obligate intracellular entities in our body. Until recently, they were only considered to be pathogens that caused a broad array of pathologies, ranging from mild disease to deaths in the most severe cases. However, recent advances in unbiased mass sequencing techniques as well as increasing epidemiological evidence have indicated that the human body is home to diverse viral species under non-pathological conditions. Despite these studies, the description of the presumably healthy viral flora, i.e. the normal human virome, is still in its infancy regarding viral composition and dynamics. This review summarizes our current knowledge of the human virome under non-pathological conditions.

Neuronal Dynamics and Axonal Flow, V. The Semisolid State of the Moving Axonal Column

PubMed Central

Weiss, Paul A.

1972-01-01

Evidence assembled since the first comprehensive description of “axonal flow”, by deformation analysis, electron microscopy, cinemicrography, and microrheology, has confirmed that the axon of the mature neuron is (a) a semisolid column; (b) in cellulifugal motion at about 1 μm/min (1 mm per day); (c) continuously reproduced at its perikaryal base; (d) propelled by a microperistaltic pulse wave in its surface; and (e) undergoing internal dissolution at the nerve ending. The axon thus “flows” as a structural entity (“axonal flow”), in contradistinction to fast “intraaxonal transport” of molecules and molecular assemblies along internal routes and by mechanisms that are still unknown. Images PMID:4111049

The viability of phantom dark energy: A review

NASA Astrophysics Data System (ADS)

Ludwick, Kevin J.

2017-09-01

In this brief review, we examine the theoretical consistency and viability of phantom dark energy. Almost all data sets from cosmological probes are compatible with the dark energy of the phantom variety (i.e. equation-of-state parameter w < -1) and may even favor evolving dark energy, and since we expect every physical entity to have some kind of field description, we set out to examine the case for phantom dark energy as a field theory. We discuss the many attempts at frameworks that may mitigate and eliminate theoretical pathologies associated with phantom dark energy. We also examine frameworks that provide an apparent measurement w < -1 while avoiding the need for a phantom field theory.

17 CFR 229.1107 - (Item 1107) Issuing entities.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 17 Commodity and Securities Exchanges 2 2011-04-01 2011-04-01 false (Item 1107) Issuing entities....1107 (Item 1107) Issuing entities. Provide the following information about the issuing entity: (a) State the issuing entity's name and describe the issuing entity's form of organization, including the...

16 CFR 801.50 - Formation of unincorporated entities.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 1 2010-01-01 2010-01-01 false Formation of unincorporated entities. 801.50... of unincorporated entities. (a) In the formation of an unincorporated entity (other than in... entity and the unincorporated entity itself may, in the formation transaction, be both acquiring and...

17 CFR 229.1107 - (Item 1107) Issuing entities.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 17 Commodity and Securities Exchanges 2 2010-04-01 2010-04-01 false (Item 1107) Issuing entities....1107 (Item 1107) Issuing entities. Provide the following information about the issuing entity: (a) State the issuing entity's name and describe the issuing entity's form of organization, including the...

16 CFR 801.50 - Formation of unincorporated entities.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 16 Commercial Practices 1 2011-01-01 2011-01-01 false Formation of unincorporated entities. 801.50... of unincorporated entities. (a) In the formation of an unincorporated entity (other than in... entity and the unincorporated entity itself may, in the formation transaction, be both acquiring and...

76 FR 66065 - Information Collection(s) Being Reviewed by the Federal Communications Commission Comments Requested

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-25

.... Respondents: Business or other for-profit entities; Federal Government; and State, Local, or Tribal Government.... Type of Review: Revision of a currently approved collection. Respondents: Business or other for-profit... information burden for small business concerns with fewer than 25 employees. The FCC may not conduct or...

Recognizing and reducing risks: HIPAA privacy and security enforcement.

PubMed

Wachler, Andrew B; Fehn, Amy K

2003-01-01

With the passing of the Health Insurance Portability and Accountability Act (HIPAA) privacy rule deadline and the security rule deadline looming, many covered entities are left wondering if they are doing enough to prevent privacy and security breaches and what type of exposure their organization could face in the event of a breach.

Period Prevalence of Acute Neck Injury in US Air Force Pilots Exposed to High G Forces

DTIC Science & Technology

1986-06-01

entities caused by irritation or compression of the cervical nerve roots. Several types of syndromes are recognized: Cervical neck muscle pain or...Spondylolysis 5. Spondylolisthesis 6. Scheuermann’s Disease ( Kyphosis ) 7. Prominent Lordosis or Kyphosis 8. Klippel-Feil Anomaly (Congenital Short Neck) 9

78 FR 33705 - Postdecisional Administrative Review Process for Occupancy or Use of National Forest System Lands...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-06-05

... DEPARTMENT OF AGRICULTURE Forest Service 36 CFR Parts 212, 214, 215, 222, 228, 241, 251, 254, and... System Lands and Resources AGENCY: USDA, Forest Service. ACTION: Final rule. SUMMARY: The United States... individuals and entities may obtain administrative review of certain types of Forest Service (Agency...

Primary renal diffuse large B-cell lymphoma with central nervous system involvement: a rare case report and literature review.

PubMed

Wang, Ying; Guo, Shuangshuang

2015-01-01

Primary renal lymphoma is a rare entity. Of these, diffuse large B-cell lymphoma is the most common pathological type and, R-CHOP regimen was the preferred chemotherapy for it. Here we present an adult case of primary renal diffuse large B-cell lymphoma.

17 CFR Appendix B to Part 145 - Schedule of Fees

Code of Federal Regulations, 2011 CFR

2011-04-01

... furnished to the requester. Fees apply to various types of requests as follows. (1) Commercial use request... search or review time. (3) Representative of the news media. Only duplication fees will be charged to any person actively gathering news for an entity that is organized and operated to publish or broadcast news...

75 FR 64684 - Cost Accounting Standards: Elimination of the Exemption From Cost Accounting Standards for...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-20

... financial accounting practices and internal controls. Consistency will be better served by all companies... such as the ownership and control of the company, and whether the contractor's accounting activities... argues that there must be some type of accounting system in foreign entities to ensure that billings...

11 CFR 104.8 - Uniform reporting of receipts.

Code of Federal Regulations, 2010 CFR

2010-01-01

... reported during the calendar year (or during the election cycle, in the case of an authorized committee... the aggregate exceeds $200 in a calendar year (or in an election cycle, in the case of an authorized... donating individual's or entity's name, mailing address, occupation or type of business, and the date of...

78 FR 49235 - Airworthiness Directives; EADS CASA (Type Certificate Previously Held by Construcciones...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-13

... invite comments on the overall regulatory, economic, environmental, and energy aspects of this proposed..., 28022 Madrid, Spain; telephone +34 91 585 55 84; fax +34 91 585 55 05; email [email protected] economic impact, positive or negative, on a substantial number of small entities under the criteria of the...

78 FR 32945 - Amendments to Regulations Governing Ocean Transportation Intermediary Licensing and Financial...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-31

... Acting as Agents for Licensed Ocean Transportation Intermediaries, 31 SRR 1058 (2009). Significant... person or entity to whom a licensed ocean freight forwarder owes a fiduciary duty. In contrast, the use... licensed ocean freight forwarder) as the principal with respect to the various types of agents that the OTI...