Active Deep Learning-Based Annotation of Electroencephalography Reports for Cohort Identification

PubMed Central

Maldonado, Ramon; Goodwin, Travis R; Harabagiu, Sanda M

2017-01-01

The annotation of a large corpus of Electroencephalography (EEG) reports is a crucial step in the development of an EEG-specific patient cohort retrieval system. The annotation of multiple types of EEG-specific medical concepts, along with their polarity and modality, is challenging, especially when automatically performed on Big Data. To address this challenge, we present a novel framework which combines the advantages of active and deep learning while producing annotations that capture a variety of attributes of medical concepts. Results obtained through our novel framework show great promise. PMID:28815135

77 FR 70456 - Receipt of Applications for Endangered Species Permits

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-26

... authorization to conduct scientific research involving capture and handling of reticulated flatwoods salamanders (Ambystoma bishop) and frosted flatwoods salamanders (Ambystoma cingulatum). This study will be conducted in...

The KIT Motion-Language Dataset.

PubMed

Plappert, Matthias; Mandery, Christian; Asfour, Tamim

2016-12-01

Linking human motion and natural language is of great interest for the generation of semantic representations of human activities as well as for the generation of robot activities based on natural language input. However, although there have been years of research in this area, no standardized and openly available data set exists to support the development and evaluation of such systems. We, therefore, propose the Karlsruhe Institute of Technology (KIT) Motion-Language Dataset, which is large, open, and extensible. We aggregate data from multiple motion capture databases and include them in our data set using a unified representation that is independent of the capture system or marker set, making it easy to work with the data regardless of its origin. To obtain motion annotations in natural language, we apply a crowd-sourcing approach and a web-based tool that was specifically build for this purpose, the Motion Annotation Tool. We thoroughly document the annotation process itself and discuss gamification methods that we used to keep annotators motivated. We further propose a novel method, perplexity-based selection, which systematically selects motions for further annotation that are either under-represented in our data set or that have erroneous annotations. We show that our method mitigates the two aforementioned problems and ensures a systematic annotation process. We provide an in-depth analysis of the structure and contents of our resulting data set, which, as of October 10, 2016, contains 3911 motions with a total duration of 11.23 hours and 6278 annotations in natural language that contain 52,903 words. We believe this makes our data set an excellent choice that enables more transparent and comparable research in this important area.

76 FR 81541 - Request for Comments Under E.O. 12898

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-28

..., agencies listed in EO 12898 signed a Memorandum of Understanding (EJ MOU), which, among other things... receipt of the information, the Department has created an Internet portal specifically designed to capture...

Annotation of UAV surveillance video

NASA Astrophysics Data System (ADS)

Howlett, Todd; Robertson, Mark A.; Manthey, Dan; Krol, John

2004-08-01

Significant progress toward the development of a video annotation capability is presented in this paper. Research and development of an object tracking algorithm applicable for UAV video is described. Object tracking is necessary for attaching the annotations to the objects of interest. A methodology and format is defined for encoding video annotations using the SMPTE Key-Length-Value encoding standard. This provides the following benefits: a non-destructive annotation, compliance with existing standards, video playback in systems that are not annotation enabled and support for a real-time implementation. A model real-time video annotation system is also presented, at a high level, using the MPEG-2 Transport Stream as the transmission medium. This work was accomplished to meet the Department of Defense"s (DoD"s) need for a video annotation capability. Current practices for creating annotated products are to capture a still image frame, annotate it using an Electric Light Table application, and then pass the annotated image on as a product. That is not adequate for reporting or downstream cueing. It is too slow and there is a severe loss of information. This paper describes a capability for annotating directly on the video.

75 FR 31812 - Receipt of Applications for Endangered Species Permits

Federal Register 2010, 2011, 2012, 2013, 2014

2010-06-04

..., and release of eastern indigo snake (Drymarchon corais couperi), reticulated flatwoods salamander (Ambystoma bishopi), and frosted flatwoods salamander (Ambystoma cingulatum) in Georgia. Applicant: Jess... authorization to: Capture and release eastern indigo snake, frosted flatwood salamander, reticulated flatwoods...

The language of gene ontology: a Zipf's law analysis.

PubMed

Kalankesh, Leila Ranandeh; Stevens, Robert; Brass, Andy

2012-06-07

Most major genome projects and sequence databases provide a GO annotation of their data, either automatically or through human annotators, creating a large corpus of data written in the language of GO. Texts written in natural language show a statistical power law behaviour, Zipf's law, the exponent of which can provide useful information on the nature of the language being used. We have therefore explored the hypothesis that collections of GO annotations will show similar statistical behaviours to natural language. Annotations from the Gene Ontology Annotation project were found to follow Zipf's law. Surprisingly, the measured power law exponents were consistently different between annotation captured using the three GO sub-ontologies in the corpora (function, process and component). On filtering the corpora using GO evidence codes we found that the value of the measured power law exponent responded in a predictable way as a function of the evidence codes used to support the annotation. Techniques from computational linguistics can provide new insights into the annotation process. GO annotations show similar statistical behaviours to those seen in natural language with measured exponents that provide a signal which correlates with the nature of the evidence codes used to support the annotations, suggesting that the measured exponent might provide a signal regarding the information content of the annotation.

Bibliography of Intelligence Literature. A Critical and Annotated Bibliography of Open-Source Literature.

DTIC Science & Technology

1985-01-01

outlooks in a continuing, important battlefield. HAREL, Isser. The House on Garibaldi Street: The First Full Account of the Capture of Adolf Eichmann ...Israeli Service, MOSSAD, describes in detailed fashion the long-range, in-depth planning and operation for the Eichmann capture by Israeli agents in

Towards Automated Annotation of Benthic Survey Images: Variability of Human Experts and Operational Modes of Automation

PubMed Central

Beijbom, Oscar; Edmunds, Peter J.; Roelfsema, Chris; Smith, Jennifer; Kline, David I.; Neal, Benjamin P.; Dunlap, Matthew J.; Moriarty, Vincent; Fan, Tung-Yung; Tan, Chih-Jui; Chan, Stephen; Treibitz, Tali; Gamst, Anthony; Mitchell, B. Greg; Kriegman, David

2015-01-01

Global climate change and other anthropogenic stressors have heightened the need to rapidly characterize ecological changes in marine benthic communities across large scales. Digital photography enables rapid collection of survey images to meet this need, but the subsequent image annotation is typically a time consuming, manual task. We investigated the feasibility of using automated point-annotation to expedite cover estimation of the 17 dominant benthic categories from survey-images captured at four Pacific coral reefs. Inter- and intra- annotator variability among six human experts was quantified and compared to semi- and fully- automated annotation methods, which are made available at coralnet.ucsd.edu. Our results indicate high expert agreement for identification of coral genera, but lower agreement for algal functional groups, in particular between turf algae and crustose coralline algae. This indicates the need for unequivocal definitions of algal groups, careful training of multiple annotators, and enhanced imaging technology. Semi-automated annotation, where 50% of the annotation decisions were performed automatically, yielded cover estimate errors comparable to those of the human experts. Furthermore, fully-automated annotation yielded rapid, unbiased cover estimates but with increased variance. These results show that automated annotation can increase spatial coverage and decrease time and financial outlay for image-based reef surveys. PMID:26154157

Calling on a million minds for community annotation in WikiProteins

PubMed Central

Mons, Barend; Ashburner, Michael; Chichester, Christine; van Mulligen, Erik; Weeber, Marc; den Dunnen, Johan; van Ommen, Gert-Jan; Musen, Mark; Cockerill, Matthew; Hermjakob, Henning; Mons, Albert; Packer, Abel; Pacheco, Roberto; Lewis, Suzanna; Berkeley, Alfred; Melton, William; Barris, Nickolas; Wales, Jimmy; Meijssen, Gerard; Moeller, Erik; Roes, Peter Jan; Borner, Katy; Bairoch, Amos

2008-01-01

WikiProteins enables community annotation in a Wiki-based system. Extracts of major data sources have been fused into an editable environment that links out to the original sources. Data from community edits create automatic copies of the original data. Semantic technology captures concepts co-occurring in one sentence and thus potential factual statements. In addition, indirect associations between concepts have been calculated. We call on a 'million minds' to annotate a 'million concepts' and to collect facts from the literature with the reward of collaborative knowledge discovery. The system is available for beta testing at . PMID:18507872

Chemical annotation of small and peptide-like molecules at the Protein Data Bank

PubMed Central

Young, Jasmine Y.; Feng, Zukang; Dimitropoulos, Dimitris; Sala, Raul; Westbrook, John; Zhuravleva, Marina; Shao, Chenghua; Quesada, Martha; Peisach, Ezra; Berman, Helen M.

2013-01-01

Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org PMID:24291661

Chemical annotation of small and peptide-like molecules at the Protein Data Bank.

PubMed

Young, Jasmine Y; Feng, Zukang; Dimitropoulos, Dimitris; Sala, Raul; Westbrook, John; Zhuravleva, Marina; Shao, Chenghua; Quesada, Martha; Peisach, Ezra; Berman, Helen M

2013-01-01

Over the past decade, the number of polymers and their complexes with small molecules in the Protein Data Bank archive (PDB) has continued to increase significantly. To support scientific advancements and ensure the best quality and completeness of the data files over the next 10 years and beyond, the Worldwide PDB partnership that manages the PDB archive is developing a new deposition and annotation system. This system focuses on efficient data capture across all supported experimental methods. The new deposition and annotation system is composed of four major modules that together support all of the processing requirements for a PDB entry. In this article, we describe one such module called the Chemical Component Annotation Tool. This tool uses information from both the Chemical Component Dictionary and Biologically Interesting molecule Reference Dictionary to aid in annotation. Benchmark studies have shown that the Chemical Component Annotation Tool provides significant improvements in processing efficiency and data quality. Database URL: http://wwpdb.org.

Center-TRACON Automation System (CTAS) En Route Trajectory Predictor Requirements and Capabilities

NASA Technical Reports Server (NTRS)

Vivona, Robert; Cate, Karen Tung

2013-01-01

This requirements framework document is designed to support the capture of requirements and capabilities for state-of-the-art trajectory predictors (TPs). This framework has been developed to assist TP experts in capturing a clear, consistent, and cross-comparable set of requirements and capabilities. The goal is to capture capabilities (types of trajectories that can be built), functional requirements (including inputs and outputs), non-functional requirements (including prediction accuracy and computational performance), approaches for constraint relaxation, and input uncertainties. The sections of this framework are based on the Common Trajectory Predictor structure developed by the FAA/Eurocontrol Cooperative R&D Action Plan 16 Committee on Common Trajectory Prediction. It is assumed that the reader is familiar with the Common TP Structure.1 This initial draft is intended as a first cut capture of the En Route TS Capabilities and Requirements. As such, it contains many annotations indicating possible logic errors in the CTAS code or in the description provided. It is intended to work out the details of the annotations with NASA and to update this document at a later time.

Standardized description of scientific evidence using the Evidence Ontology (ECO)

PubMed Central

Chibucos, Marcus C.; Mungall, Christopher J.; Balakrishnan, Rama; Christie, Karen R.; Huntley, Rachael P.; White, Owen; Blake, Judith A.; Lewis, Suzanna E.; Giglio, Michelle

2014-01-01

The Evidence Ontology (ECO) is a structured, controlled vocabulary for capturing evidence in biological research. ECO includes diverse terms for categorizing evidence that supports annotation assertions including experimental types, computational methods, author statements and curator inferences. Using ECO, annotation assertions can be distinguished according to the evidence they are based on such as those made by curators versus those automatically computed or those made via high-throughput data review versus single test experiments. Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics, Saccharomyces Genome Database, PomBase, the Protein Information Resource and others. Information on the development and use of ECO can be found at http://evidenceontology.org. The ontology is freely available under Creative Commons license (CC BY-SA 3.0), and can be downloaded in both Open Biological Ontologies and Web Ontology Language formats at http://code.google.com/p/evidenceontology. Also at this site is a tracker for user submission of term requests and questions. ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources. Database URL: Evidence Ontology Web site: http://evidenceontology.org PMID:25052702

3D facial landmarks: Inter-operator variability of manual annotation

PubMed Central

2014-01-01

Background Manual annotation of landmarks is a known source of variance, which exist in all fields of medical imaging, influencing the accuracy and interpretation of the results. However, the variability of human facial landmarks is only sparsely addressed in the current literature as opposed to e.g. the research fields of orthodontics and cephalometrics. We present a full facial 3D annotation procedure and a sparse set of manually annotated landmarks, in effort to reduce operator time and minimize the variance. Method Facial scans from 36 voluntary unrelated blood donors from the Danish Blood Donor Study was randomly chosen. Six operators twice manually annotated 73 anatomical and pseudo-landmarks, using a three-step scheme producing a dense point correspondence map. We analyzed both the intra- and inter-operator variability, using mixed-model ANOVA. We then compared four sparse sets of landmarks in order to construct a dense correspondence map of the 3D scans with a minimum point variance. Results The anatomical landmarks of the eye were associated with the lowest variance, particularly the center of the pupils. Whereas points of the jaw and eyebrows have the highest variation. We see marginal variability in regards to intra-operator and portraits. Using a sparse set of landmarks (n=14), that capture the whole face, the dense point mean variance was reduced from 1.92 to 0.54 mm. Conclusion The inter-operator variability was primarily associated with particular landmarks, where more leniently landmarks had the highest variability. The variables embedded in the portray and the reliability of a trained operator did only have marginal influence on the variability. Further, using 14 of the annotated landmarks we were able to reduced the variability and create a dense correspondences mesh to capture all facial features. PMID:25306436

Annotating spatio-temporal datasets for meaningful analysis in the Web

NASA Astrophysics Data System (ADS)

Stasch, Christoph; Pebesma, Edzer; Scheider, Simon

2014-05-01

More and more environmental datasets that vary in space and time are available in the Web. This comes along with an advantage of using the data for other purposes than originally foreseen, but also with the danger that users may apply inappropriate analysis procedures due to lack of important assumptions made during the data collection process. In order to guide towards a meaningful (statistical) analysis of spatio-temporal datasets available in the Web, we have developed a Higher-Order-Logic formalism that captures some relevant assumptions in our previous work [1]. It allows to proof on meaningful spatial prediction and aggregation in a semi-automated fashion. In this poster presentation, we will present a concept for annotating spatio-temporal datasets available in the Web with concepts defined in our formalism. Therefore, we have defined a subset of the formalism as a Web Ontology Language (OWL) pattern. It allows capturing the distinction between the different spatio-temporal variable types, i.e. point patterns, fields, lattices and trajectories, that in turn determine whether a particular dataset can be interpolated or aggregated in a meaningful way using a certain procedure. The actual annotations that link spatio-temporal datasets with the concepts in the ontology pattern are provided as Linked Data. In order to allow data producers to add the annotations to their datasets, we have implemented a Web portal that uses a triple store at the backend to store the annotations and to make them available in the Linked Data cloud. Furthermore, we have implemented functions in the statistical environment R to retrieve the RDF annotations and, based on these annotations, to support a stronger typing of spatio-temporal datatypes guiding towards a meaningful analysis in R. [1] Stasch, C., Scheider, S., Pebesma, E., Kuhn, W. (2014): "Meaningful spatial prediction and aggregation", Environmental Modelling & Software, 51, 149-165.

Document image retrieval through word shape coding.

PubMed

Lu, Shijian; Li, Linlin; Tan, Chew Lim

2008-11-01

This paper presents a document retrieval technique that is capable of searching document images without OCR (optical character recognition). The proposed technique retrieves document images by a new word shape coding scheme, which captures the document content through annotating each word image by a word shape code. In particular, we annotate word images by using a set of topological shape features including character ascenders/descenders, character holes, and character water reservoirs. With the annotated word shape codes, document images can be retrieved by either query keywords or a query document image. Experimental results show that the proposed document image retrieval technique is fast, efficient, and tolerant to various types of document degradation.

Collaborative Workspaces within Distributed Virtual Environments.

DTIC Science & Technology

1996-12-01

such as a text document, a 3D model, or a captured image using a collaborative workspace called the InPerson Whiteboard . The Whiteboard contains a...commands for editing objects drawn on the screen. Finally, when the call is completed, the Whiteboard can be saved to a file for future use . IRIS Annotator... use , and a shared whiteboard that includes a number of multimedia annotation tools. Both systems are also mindful of bandwidth limitations and can

Applying Content Management to Automated Provenance Capture

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

Schuchardt, Karen L.; Gibson, Tara D.; Stephan, Eric G.

2008-04-10

Workflows and data pipelines are becoming increasingly valuable in both computational and experimen-tal sciences. These automated systems are capable of generating significantly more data within the same amount of time than their manual counterparts. Automatically capturing and recording data prove-nance and annotation as part of these workflows is critical for data management, verification, and dis-semination. Our goal in addressing the provenance challenge was to develop and end-to-end system that demonstrates real-time capture, persistent content management, and ad-hoc searches of both provenance and metadata using open source software and standard protocols. We describe our prototype, which extends the Kepler workflow toolsmore » for the execution environment, the Scientific Annotation Middleware (SAM) content management software for data services, and an existing HTTP-based query protocol. Our implementation offers several unique capabilities, and through the use of standards, is able to pro-vide access to the provenance record to a variety of commonly available client tools.« less

45 CFR 506.1 - “Civilian American citizen” defined.

Code of Federal Regulations, 2014 CFR

2014-10-01

... COMMISSION OF THE UNITED STATES, DEPARTMENT OF JUSTICE RECEIPT, ADMINISTRATION, AND PAYMENT OF CLAIMS UNDER TITLE I OF THE WAR CLAIMS ACT OF 1948, AS AMENDED ELIGIBILITY REQUIREMENTS FOR COMPENSATION Civilian... who, being then a citizen of the United States, was captured in Southeast Asia during the Vietnam...

45 CFR 506.1 - “Civilian American citizen” defined.

Code of Federal Regulations, 2011 CFR

2011-10-01

... COMMISSION OF THE UNITED STATES, DEPARTMENT OF JUSTICE RECEIPT, ADMINISTRATION, AND PAYMENT OF CLAIMS UNDER TITLE I OF THE WAR CLAIMS ACT OF 1948, AS AMENDED ELIGIBILITY REQUIREMENTS FOR COMPENSATION Civilian... who, being then a citizen of the United States, was captured in Southeast Asia during the Vietnam...

45 CFR 506.1 - “Civilian American citizen” defined.

Code of Federal Regulations, 2012 CFR

2012-10-01

... COMMISSION OF THE UNITED STATES, DEPARTMENT OF JUSTICE RECEIPT, ADMINISTRATION, AND PAYMENT OF CLAIMS UNDER TITLE I OF THE WAR CLAIMS ACT OF 1948, AS AMENDED ELIGIBILITY REQUIREMENTS FOR COMPENSATION Civilian... who, being then a citizen of the United States, was captured in Southeast Asia during the Vietnam...

45 CFR 506.1 - “Civilian American citizen” defined.

Code of Federal Regulations, 2013 CFR

2013-10-01

... COMMISSION OF THE UNITED STATES, DEPARTMENT OF JUSTICE RECEIPT, ADMINISTRATION, AND PAYMENT OF CLAIMS UNDER TITLE I OF THE WAR CLAIMS ACT OF 1948, AS AMENDED ELIGIBILITY REQUIREMENTS FOR COMPENSATION Civilian... who, being then a citizen of the United States, was captured in Southeast Asia during the Vietnam...

The caBIG annotation and image Markup project.

PubMed

Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Sepukar, Kastubh; Rubin, Daniel L

2010-04-01

Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM.

BioCreative V CDR task corpus: a resource for chemical disease relation extraction.

PubMed

Li, Jiao; Sun, Yueping; Johnson, Robin J; Sciaky, Daniela; Wei, Chih-Hsuan; Leaman, Robert; Davis, Allan Peter; Mattingly, Carolyn J; Wiegers, Thomas C; Lu, Zhiyong

2016-01-01

Community-run, formal evaluations and manually annotated text corpora are critically important for advancing biomedical text-mining research. Recently in BioCreative V, a new challenge was organized for the tasks of disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. Given the nature of both tasks, a test collection is required to contain both disease/chemical annotations and relation annotations in the same set of articles. Despite previous efforts in biomedical corpus construction, none was found to be sufficient for the task. Thus, we developed our own corpus called BC5CDR during the challenge by inviting a team of Medical Subject Headings (MeSH) indexers for disease/chemical entity annotation and Comparative Toxicogenomics Database (CTD) curators for CID relation annotation. To ensure high annotation quality and productivity, detailed annotation guidelines and automatic annotation tools were provided. The resulting BC5CDR corpus consists of 1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions. Each entity annotation includes both the mention text spans and normalized concept identifiers, using MeSH as the controlled vocabulary. To ensure accuracy, the entities were first captured independently by two annotators followed by a consensus annotation: The average inter-annotator agreement (IAA) scores were 87.49% and 96.05% for the disease and chemicals, respectively, in the test set according to the Jaccard similarity coefficient. Our corpus was successfully used for the BioCreative V challenge tasks and should serve as a valuable resource for the text-mining research community.Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/. Published by Oxford University Press 2016. This work is written by US Government employees and is in the public domain in the United States.

Self-Reported Functional Status among the Old-Old: A Comparison of Two Israeli Cohorts

PubMed Central

Litwin, Howard; Shrira, Amit; Shmotkin, Dov

2012-01-01

OBJECTIVES To examine differences in functional status among two successive cohorts. METHODS The study was a comparative analysis of Jewish respondents aged 75–94 from two nationwide random samples: the Cross-Sectional and Longitudinal Aging Study (1989–1992; N =1200) and the Survey of Health, Ageing, and Retirement in Europe (2005–2006; N =379). Self-reported functional limitation and disability were compared by means of logistic regressions and MANCOVA, controlling for age, gender, origin, education, marital status, income, self-rated health, and home care receipt. RESULTS Reported functional limitation decreased in the later cohort (SHARE-Israel), but ADL- and IADL-disability increased. Receipt of home care moderated these effects. ADL- and IADL-disability increased among home-care-receiving respondents in the later cohort whereas functional limitation decreased among respondents not in receipt of home care. DISCUSSION The findings suggest that different measures used to assess the disablement process capture different aspects, and that contextual factors influence how older people rate their own functional capacity. PMID:22422761

75 FR 14154 - Notice of Receipt of Several Pesticide Petitions Filed for Residues of Pesticide Chemicals in or...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-24

... for plant commodities) are both gas liquid chromatography (GLC) methods with electron capture... analytical methodology using liquid chromatography/mass spectrometry/mass spectrometry (LC/MS/MS) detection...-aminopropane]) using gas chromatography (GC) have been submitted to the EPA. In addition, a new validated...

A Semantic Web-based System for Mining Genetic Mutations in Cancer Clinical Trials.

PubMed

Priya, Sambhawa; Jiang, Guoqian; Dasari, Surendra; Zimmermann, Michael T; Wang, Chen; Heflin, Jeff; Chute, Christopher G

2015-01-01

Textual eligibility criteria in clinical trial protocols contain important information about potential clinically relevant pharmacogenomic events. Manual curation for harvesting this evidence is intractable as it is error prone and time consuming. In this paper, we develop and evaluate a Semantic Web-based system that captures and manages mutation evidences and related contextual information from cancer clinical trials. The system has 2 main components: an NLP-based annotator and a Semantic Web ontology-based annotation manager. We evaluated the performance of the annotator in terms of precision and recall. We demonstrated the usefulness of the system by conducting case studies in retrieving relevant clinical trials using a collection of mutations identified from TCGA Leukemia patients and Atlas of Genetics and Cytogenetics in Oncology and Haematology. In conclusion, our system using Semantic Web technologies provides an effective framework for extraction, annotation, standardization and management of genetic mutations in cancer clinical trials.

GFam: a platform for automatic annotation of gene families.

PubMed

Sasidharan, Rajkumar; Nepusz, Tamás; Swarbreck, David; Huala, Eva; Paccanaro, Alberto

2012-10-01

We have developed GFam, a platform for automatic annotation of gene/protein families. GFam provides a framework for genome initiatives and model organism resources to build domain-based families, derive meaningful functional labels and offers a seamless approach to propagate functional annotation across periodic genome updates. GFam is a hybrid approach that uses a greedy algorithm to chain component domains from InterPro annotation provided by its 12 member resources followed by a sequence-based connected component analysis of un-annotated sequence regions to derive consensus domain architecture for each sequence and subsequently generate families based on common architectures. Our integrated approach increases sequence coverage by 7.2 percentage points and residue coverage by 14.6 percentage points higher than the coverage relative to the best single-constituent database within InterPro for the proteome of Arabidopsis. The true power of GFam lies in maximizing annotation provided by the different InterPro data sources that offer resource-specific coverage for different regions of a sequence. GFam's capability to capture higher sequence and residue coverage can be useful for genome annotation, comparative genomics and functional studies. GFam is a general-purpose software and can be used for any collection of protein sequences. The software is open source and can be obtained from http://www.paccanarolab.org/software/gfam/.

Crowdtruth validation: a new paradigm for validating algorithms that rely on image correspondences.

PubMed

Maier-Hein, Lena; Kondermann, Daniel; Roß, Tobias; Mersmann, Sven; Heim, Eric; Bodenstedt, Sebastian; Kenngott, Hannes Götz; Sanchez, Alexandro; Wagner, Martin; Preukschas, Anas; Wekerle, Anna-Laura; Helfert, Stefanie; März, Keno; Mehrabi, Arianeb; Speidel, Stefanie; Stock, Christian

2015-08-01

Feature tracking and 3D surface reconstruction are key enabling techniques to computer-assisted minimally invasive surgery. One of the major bottlenecks related to training and validation of new algorithms is the lack of large amounts of annotated images that fully capture the wide range of anatomical/scene variance in clinical practice. To address this issue, we propose a novel approach to obtaining large numbers of high-quality reference image annotations at low cost in an extremely short period of time. The concept is based on outsourcing the correspondence search to a crowd of anonymous users from an online community (crowdsourcing) and comprises four stages: (1) feature detection, (2) correspondence search via crowdsourcing, (3) merging multiple annotations per feature by fitting Gaussian finite mixture models, (4) outlier removal using the result of the clustering as input for a second annotation task. On average, 10,000 annotations were obtained within 24 h at a cost of $100. The annotation of the crowd after clustering and before outlier removal was of expert quality with a median distance of about 1 pixel to a publically available reference annotation. The threshold for the outlier removal task directly determines the maximum annotation error, but also the number of points removed. Our concept is a novel and effective method for fast, low-cost and highly accurate correspondence generation that could be adapted to various other applications related to large-scale data annotation in medical image computing and computer-assisted interventions.

Direct Observation of the Behaviour of Females with Rett Syndrome.

PubMed

Cianfaglione, Rina; Meek, Andrea; Clarke, Angus; Kerr, Michael; Hastings, Richard P; Felce, David

The aim was to observe the behaviour of a sample of females with RTT and explore how it was organized in relation to environmental events. Ten participants, all with a less severe form of classic ( n  = 9) or atypical ( n  = 1) Rett syndrome (RTT), were filmed at home and at school or day centre. Analysis used real-time data capture software. Observational categories distinguished engagement in social and non-social pursuits, hand stereotypies, self-injury and the receipt of attention from a parent, teacher or carer. Associations between participant behaviour and intake variables and receipt of attention were explored. Concurrent and lagged conditional probabilities between behavioural categories and receipt of attention were calculated. Receipt of adult attention was high. Engagement in activity using the hands was associated with a less severe condition and greater developmental age. Engagement in activity, whether using the hands or not, and social engagement were positively associated with receipt of support. The extent of hand stereotypies varied greatly across participants but was independent of environmental events. Six participants self-injured. There was some evidence that self-injury was related to adult attention. Participants appeared to experience a carer and attention rich environment and their levels of engagement seemed high as a result. As in the more general literature, engagement in activity was related to personal development and to social support. Self-injury contrasted with hand stereotypies in having possible environmental function.

Annotation of rule-based models with formal semantics to enable creation, analysis, reuse and visualization.

PubMed

Misirli, Goksel; Cavaliere, Matteo; Waites, William; Pocock, Matthew; Madsen, Curtis; Gilfellon, Owen; Honorato-Zimmer, Ricardo; Zuliani, Paolo; Danos, Vincent; Wipat, Anil

2016-03-15

Biological systems are complex and challenging to model and therefore model reuse is highly desirable. To promote model reuse, models should include both information about the specifics of simulations and the underlying biology in the form of metadata. The availability of computationally tractable metadata is especially important for the effective automated interpretation and processing of models. Metadata are typically represented as machine-readable annotations which enhance programmatic access to information about models. Rule-based languages have emerged as a modelling framework to represent the complexity of biological systems. Annotation approaches have been widely used for reaction-based formalisms such as SBML. However, rule-based languages still lack a rich annotation framework to add semantic information, such as machine-readable descriptions, to the components of a model. We present an annotation framework and guidelines for annotating rule-based models, encoded in the commonly used Kappa and BioNetGen languages. We adapt widely adopted annotation approaches to rule-based models. We initially propose a syntax to store machine-readable annotations and describe a mapping between rule-based modelling entities, such as agents and rules, and their annotations. We then describe an ontology to both annotate these models and capture the information contained therein, and demonstrate annotating these models using examples. Finally, we present a proof of concept tool for extracting annotations from a model that can be queried and analyzed in a uniform way. The uniform representation of the annotations can be used to facilitate the creation, analysis, reuse and visualization of rule-based models. Although examples are given, using specific implementations the proposed techniques can be applied to rule-based models in general. The annotation ontology for rule-based models can be found at http://purl.org/rbm/rbmo The krdf tool and associated executable examples are available at http://purl.org/rbm/rbmo/krdf anil.wipat@newcastle.ac.uk or vdanos@inf.ed.ac.uk. © The Author 2015. Published by Oxford University Press.

Receipt of Cancer Screening Is a Predictor of Life Expectancy.

PubMed

Goodwin, James S; Sheffield, Kristin; Li, Shuang; Tan, Alai

2016-11-01

Obtaining cancer screening on patients with limited life expectancy has been proposed as a measure for low quality care for primary care physicians (PCPs). However, administrative data may underestimate life expectancy in patients who undergo screening. To determine the association between receipt of screening mammography or PSA and overall survival. Retrospective cohort study from 1/1/1999 to 12/31/2012. Receipt of screening was assessed for 2001-2002 and survival from 1/1/2003 to 12/31/2012. Life expectancy was estimated as of 1/1/03 using a validated algorithm, and was compared to actual survival for men and women, stratified by receipt of cancer screening. A 5 % sample of Medicare beneficiaries aged 69-90 years as of 1/1/2003 (n = 906,723). Receipt of screening mammography in 2001-2002 for women, or a screening PSA test in 2002 for men. Survival from 1/1/2003 through 12/31/2012. Subjects were stratified by life expectancy based on age and comorbidity. Within each stratum, the subjects with prior cancer screening had actual median survivals higher than those who were not screened, with differences ranging from 1.7 to 2.1 years for women and 0.9 to 1.1 years for men. In a Cox model, non-receipt of screening in women had an impact on survival (HR = 1.52; 95 % CI = 1.51, 1.54) similar in magnitude to a diagnosis of complicated diabetes or heart failure, and was comparable to uncomplicated diabetes or liver disease in men (HR = 1.23; 1.22, 1.25). Receipt of cancer screening is a powerful marker of health status that is not captured by comorbidity measures in administrative data. Because life expectancy algorithms using administrative data underestimate the life expectancy of patients who undergo screening, they can overestimate the problem of cancer screening in patients with limited life expectancy.

Generating Customized Verifiers for Automatically Generated Code

NASA Technical Reports Server (NTRS)

Denney, Ewen; Fischer, Bernd

2008-01-01

Program verification using Hoare-style techniques requires many logical annotations. We have previously developed a generic annotation inference algorithm that weaves in all annotations required to certify safety properties for automatically generated code. It uses patterns to capture generator- and property-specific code idioms and property-specific meta-program fragments to construct the annotations. The algorithm is customized by specifying the code patterns and integrating them with the meta-program fragments for annotation construction. However, this is difficult since it involves tedious and error-prone low-level term manipulations. Here, we describe an annotation schema compiler that largely automates this customization task using generative techniques. It takes a collection of high-level declarative annotation schemas tailored towards a specific code generator and safety property, and generates all customized analysis functions and glue code required for interfacing with the generic algorithm core, thus effectively creating a customized annotation inference algorithm. The compiler raises the level of abstraction and simplifies schema development and maintenance. It also takes care of some more routine aspects of formulating patterns and schemas, in particular handling of irrelevant program fragments and irrelevant variance in the program structure, which reduces the size, complexity, and number of different patterns and annotation schemas that are required. The improvements described here make it easier and faster to customize the system to a new safety property or a new generator, and we demonstrate this by customizing it to certify frame safety of space flight navigation code that was automatically generated from Simulink models by MathWorks' Real-Time Workshop.

CARMA: Software for continuous affect rating and media annotation

PubMed Central

Girard, Jeffrey M

2017-01-01

CARMA is a media annotation program that collects continuous ratings while displaying audio and video files. It is designed to be highly user-friendly and easily customizable. Based on Gottman and Levenson's affect rating dial, CARMA enables researchers and study participants to provide moment-by-moment ratings of multimedia files using a computer mouse or keyboard. The rating scale can be configured on a number of parameters including the labels for its upper and lower bounds, its numerical range, and its visual representation. Annotations can be displayed alongside the multimedia file and saved for easy import into statistical analysis software. CARMA provides a tool for researchers in affective computing, human-computer interaction, and the social sciences who need to capture the unfolding of subjective experience and observable behavior over time. PMID:29308198

CommWalker: correctly evaluating modules in molecular networks in light of annotation bias.

PubMed

Luecken, M D; Page, M J T; Crosby, A J; Mason, S; Reinert, G; Deane, C M

2018-03-15

Detecting novel functional modules in molecular networks is an important step in biological research. In the absence of gold standard functional modules, functional annotations are often used to verify whether detected modules/communities have biological meaning. However, as we show, the uneven distribution of functional annotations means that such evaluation methods favor communities of well-studied proteins. We propose a novel framework for the evaluation of communities as functional modules. Our proposed framework, CommWalker, takes communities as inputs and evaluates them in their local network environment by performing short random walks. We test CommWalker's ability to overcome annotation bias using input communities from four community detection methods on two protein interaction networks. We find that modules accepted by CommWalker are similarly co-expressed as those accepted by current methods. Crucially, CommWalker performs well not only in well-annotated regions, but also in regions otherwise obscured by poor annotation. CommWalker community prioritization both faithfully captures well-validated communities and identifies functional modules that may correspond to more novel biology. The CommWalker algorithm is freely available at opig.stats.ox.ac.uk/resources or as a docker image on the Docker Hub at hub.docker.com/r/lueckenmd/commwalker/. deane@stats.ox.ac.uk. Supplementary data are available at Bioinformatics online.

Feeding Forward: Using Feedback to Promote Student Reflection and Learning--A Teaching Model

ERIC Educational Resources Information Center

Quinton, Sarah; Smallbone, Teresa

2010-01-01

Engaging in reflection is a vital part of learning for university students and its practice should be embedded in course design. Feedback on written work can be used as a vehicle for reflection. Both the gift and receipt of feedback and the habit of reflection require practice and capturing this experiential learning can be achieved in a class…

Text recognition and correction for automated data collection by mobile devices

NASA Astrophysics Data System (ADS)

Ozarslan, Suleyman; Eren, P. Erhan

2014-03-01

Participatory sensing is an approach which allows mobile devices such as mobile phones to be used for data collection, analysis and sharing processes by individuals. Data collection is the first and most important part of a participatory sensing system, but it is time consuming for the participants. In this paper, we discuss automatic data collection approaches for reducing the time required for collection, and increasing the amount of collected data. In this context, we explore automated text recognition on images of store receipts which are captured by mobile phone cameras, and the correction of the recognized text. Accordingly, our first goal is to evaluate the performance of the Optical Character Recognition (OCR) method with respect to data collection from store receipt images. Images captured by mobile phones exhibit some typical problems, and common image processing methods cannot handle some of them. Consequently, the second goal is to address these types of problems through our proposed Knowledge Based Correction (KBC) method used in support of the OCR, and also to evaluate the KBC method with respect to the improvement on the accurate recognition rate. Results of the experiments show that the KBC method improves the accurate data recognition rate noticeably.

A Bayesian network coding scheme for annotating biomedical information presented to genetic counseling clients.

PubMed

Green, Nancy

2005-04-01

We developed a Bayesian network coding scheme for annotating biomedical content in layperson-oriented clinical genetics documents. The coding scheme supports the representation of probabilistic and causal relationships among concepts in this domain, at a high enough level of abstraction to capture commonalities among genetic processes and their relationship to health. We are using the coding scheme to annotate a corpus of genetic counseling patient letters as part of the requirements analysis and knowledge acquisition phase of a natural language generation project. This paper describes the coding scheme and presents an evaluation of intercoder reliability for its tag set. In addition to giving examples of use of the coding scheme for analysis of discourse and linguistic features in this genre, we suggest other uses for it in analysis of layperson-oriented text and dialogue in medical communication.

The RNA-binding protein repertoire of embryonic stem cells.

PubMed

Kwon, S Chul; Yi, Hyerim; Eichelbaum, Katrin; Föhr, Sophia; Fischer, Bernd; You, Kwon Tae; Castello, Alfredo; Krijgsveld, Jeroen; Hentze, Matthias W; Kim, V Narry

2013-09-01

RNA-binding proteins (RBPs) have essential roles in RNA-mediated gene regulation, and yet annotation of RBPs is limited mainly to those with known RNA-binding domains. To systematically identify the RBPs of embryonic stem cells (ESCs), we here employ interactome capture, which combines UV cross-linking of RBP to RNA in living cells, oligo(dT) capture and MS. From mouse ESCs (mESCs), we have defined 555 proteins constituting the mESC mRNA interactome, including 283 proteins not previously annotated as RBPs. Of these, 68 new RBP candidates are highly expressed in ESCs compared to differentiated cells, implicating a role in stem-cell physiology. Two well-known E3 ubiquitin ligases, Trim25 (also called Efp) and Trim71 (also called Lin41), are validated as RBPs, revealing a potential link between RNA biology and protein-modification pathways. Our study confirms and expands the atlas of RBPs, providing a useful resource for the study of the RNA-RBP network in stem cells.

Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

NASA Astrophysics Data System (ADS)

Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

2006-12-01

Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

Methods for eliciting, annotating, and analyzing databases for child speech development.

PubMed

Beckman, Mary E; Plummer, Andrew R; Munson, Benjamin; Reidy, Patrick F

2017-09-01

Methods from automatic speech recognition (ASR), such as segmentation and forced alignment, have facilitated the rapid annotation and analysis of very large adult speech databases and databases of caregiver-infant interaction, enabling advances in speech science that were unimaginable just a few decades ago. This paper centers on two main problems that must be addressed in order to have analogous resources for developing and exploiting databases of young children's speech. The first problem is to understand and appreciate the differences between adult and child speech that cause ASR models developed for adult speech to fail when applied to child speech. These differences include the fact that children's vocal tracts are smaller than those of adult males and also changing rapidly in size and shape over the course of development, leading to between-talker variability across age groups that dwarfs the between-talker differences between adult men and women. Moreover, children do not achieve fully adult-like speech motor control until they are young adults, and their vocabularies and phonological proficiency are developing as well, leading to considerably more within-talker variability as well as more between-talker variability. The second problem then is to determine what annotation schemas and analysis techniques can most usefully capture relevant aspects of this variability. Indeed, standard acoustic characterizations applied to child speech reveal that adult-centered annotation schemas fail to capture phenomena such as the emergence of covert contrasts in children's developing phonological systems, while also revealing children's nonuniform progression toward community speech norms as they acquire the phonological systems of their native languages. Both problems point to the need for more basic research into the growth and development of the articulatory system (as well as of the lexicon and phonological system) that is oriented explicitly toward the construction of age-appropriate computational models.

Nonlinear Deep Kernel Learning for Image Annotation.

PubMed

Jiu, Mingyuan; Sahbi, Hichem

2017-02-08

Multiple kernel learning (MKL) is a widely used technique for kernel design. Its principle consists in learning, for a given support vector classifier, the most suitable convex (or sparse) linear combination of standard elementary kernels. However, these combinations are shallow and often powerless to capture the actual similarity between highly semantic data, especially for challenging classification tasks such as image annotation. In this paper, we redefine multiple kernels using deep multi-layer networks. In this new contribution, a deep multiple kernel is recursively defined as a multi-layered combination of nonlinear activation functions, each one involves a combination of several elementary or intermediate kernels, and results into a positive semi-definite deep kernel. We propose four different frameworks in order to learn the weights of these networks: supervised, unsupervised, kernel-based semisupervised and Laplacian-based semi-supervised. When plugged into support vector machines (SVMs), the resulting deep kernel networks show clear gain, compared to several shallow kernels for the task of image annotation. Extensive experiments and analysis on the challenging ImageCLEF photo annotation benchmark, the COREL5k database and the Banana dataset validate the effectiveness of the proposed method.

iPad: Semantic annotation and markup of radiological images.

PubMed

Rubin, Daniel L; Rodriguez, Cesar; Shah, Priyanka; Beaulieu, Chris

2008-11-06

Radiological images contain a wealth of information,such as anatomy and pathology, which is often not explicit and computationally accessible. Information schemes are being developed to describe the semantic content of images, but such schemes can be unwieldy to operationalize because there are few tools to enable users to capture structured information easily as part of the routine research workflow. We have created iPad, an open source tool enabling researchers and clinicians to create semantic annotations on radiological images. iPad hides the complexity of the underlying image annotation information model from users, permitting them to describe images and image regions using a graphical interface that maps their descriptions to structured ontologies semi-automatically. Image annotations are saved in a variety of formats,enabling interoperability among medical records systems, image archives in hospitals, and the Semantic Web. Tools such as iPad can help reduce the burden of collecting structured information from images, and it could ultimately enable researchers and physicians to exploit images on a very large scale and glean the biological and physiological significance of image content.

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space

PubMed Central

Schnoes, Alexandra M.; Ream, David C.; Thorman, Alexander W.; Babbitt, Patricia C.; Friedberg, Iddo

2013-01-01

The ongoing functional annotation of proteins relies upon the work of curators to capture experimental findings from scientific literature and apply them to protein sequence and structure data. However, with the increasing use of high-throughput experimental assays, a small number of experimental studies dominate the functional protein annotations collected in databases. Here, we investigate just how prevalent is the “few articles - many proteins” phenomenon. We examine the experimentally validated annotation of proteins provided by several groups in the GO Consortium, and show that the distribution of proteins per published study is exponential, with 0.14% of articles providing the source of annotations for 25% of the proteins in the UniProt-GOA compilation. Since each of the dominant articles describes the use of an assay that can find only one function or a small group of functions, this leads to substantial biases in what we know about the function of many proteins. Mass-spectrometry, microscopy and RNAi experiments dominate high throughput experiments. Consequently, the functional information derived from these experiments is mostly of the subcellular location of proteins, and of the participation of proteins in embryonic developmental pathways. For some organisms, the information provided by different studies overlap by a large amount. We also show that the information provided by high throughput experiments is less specific than those provided by low throughput experiments. Given the experimental techniques available, certain biases in protein function annotation due to high-throughput experiments are unavoidable. Knowing that these biases exist and understanding their characteristics and extent is important for database curators, developers of function annotation programs, and anyone who uses protein function annotation data to plan experiments. PMID:23737737

Challenges in discriminating profanity from hate speech

NASA Astrophysics Data System (ADS)

Malmasi, Shervin; Zampieri, Marcos

2018-03-01

In this study, we approach the problem of distinguishing general profanity from hate speech in social media, something which has not been widely considered. Using a new dataset annotated specifically for this task, we employ supervised classification along with a set of features that includes ?-grams, skip-grams and clustering-based word representations. We apply approaches based on single classifiers as well as more advanced ensemble classifiers and stacked generalisation, achieving the best result of ? accuracy for this 3-class classification task. Analysis of the results reveals that discriminating hate speech and profanity is not a simple task, which may require features that capture a deeper understanding of the text not always possible with surface ?-grams. The variability of gold labels in the annotated data, due to differences in the subjective adjudications of the annotators, is also an issue. Other directions for future work are discussed.

Detection and enforcement of failure-to-yield in an emergency vehicle preemption system

NASA Technical Reports Server (NTRS)

Bachelder, Aaron (Inventor); Wickline, Richard (Inventor)

2007-01-01

An intersection controlled by an intersection controller receives trigger signals from on-coming emergency vehicles responding to an emergency call. The intersection controller initiates surveillance of the intersection via cameras installed at the intersection in response to a received trigger signal. The surveillance may begin immediately upon receipt of the trigger signal from an emergency vehicle, or may wait until the intersection controller determines that the signaling emergency vehicle is in the field of view of the cameras at the intersection. Portions of the captured images are tagged by the intersection controller based on tag signals transmitted by the vehicle or based on detected traffic patterns that indicate a potential traffic violation. The captured images are downloaded to a processing facility that analyzes the images and automatically issues citations for captured traffic violations.

Optical character recognition of camera-captured images based on phase features

NASA Astrophysics Data System (ADS)

Diaz-Escobar, Julia; Kober, Vitaly

2015-09-01

Nowadays most of digital information is obtained using mobile devices specially smartphones. In particular, it brings the opportunity for optical character recognition in camera-captured images. For this reason many recognition applications have been recently developed such as recognition of license plates, business cards, receipts and street signal; document classification, augmented reality, language translator and so on. Camera-captured images are usually affected by geometric distortions, nonuniform illumination, shadow, noise, which make difficult the recognition task with existing systems. It is well known that the Fourier phase contains a lot of important information regardless of the Fourier magnitude. So, in this work we propose a phase-based recognition system exploiting phase-congruency features for illumination/scale invariance. The performance of the proposed system is tested in terms of miss classifications and false alarms with the help of computer simulation.

Determining similarity of scientific entities in annotation datasets

PubMed Central

Palma, Guillermo; Vidal, Maria-Esther; Haag, Eric; Raschid, Louiqa; Thor, Andreas

2015-01-01

Linked Open Data initiatives have made available a diversity of scientific collections where scientists have annotated entities in the datasets with controlled vocabulary terms from ontologies. Annotations encode scientific knowledge, which is captured in annotation datasets. Determining relatedness between annotated entities becomes a building block for pattern mining, e.g. identifying drug–drug relationships may depend on the similarity of the targets that interact with each drug. A diversity of similarity measures has been proposed in the literature to compute relatedness between a pair of entities. Each measure exploits some knowledge including the name, function, relationships with other entities, taxonomic neighborhood and semantic knowledge. We propose a novel general-purpose annotation similarity measure called ‘AnnSim’ that measures the relatedness between two entities based on the similarity of their annotations. We model AnnSim as a 1–1 maximum weight bipartite match and exploit properties of existing solvers to provide an efficient solution. We empirically study the performance of AnnSim on real-world datasets of drugs and disease associations from clinical trials and relationships between drugs and (genomic) targets. Using baselines that include a variety of measures, we identify where AnnSim can provide a deeper understanding of the semantics underlying the relatedness of a pair of entities or where it could lead to predicting new links or identifying potential novel patterns. Although AnnSim does not exploit knowledge or properties of a particular domain, its performance compares well with a variety of state-of-the-art domain-specific measures. Database URL: http://www.yeastgenome.org/ PMID:25725057

Determining similarity of scientific entities in annotation datasets.

PubMed

Palma, Guillermo; Vidal, Maria-Esther; Haag, Eric; Raschid, Louiqa; Thor, Andreas

2015-01-01

Linked Open Data initiatives have made available a diversity of scientific collections where scientists have annotated entities in the datasets with controlled vocabulary terms from ontologies. Annotations encode scientific knowledge, which is captured in annotation datasets. Determining relatedness between annotated entities becomes a building block for pattern mining, e.g. identifying drug-drug relationships may depend on the similarity of the targets that interact with each drug. A diversity of similarity measures has been proposed in the literature to compute relatedness between a pair of entities. Each measure exploits some knowledge including the name, function, relationships with other entities, taxonomic neighborhood and semantic knowledge. We propose a novel general-purpose annotation similarity measure called 'AnnSim' that measures the relatedness between two entities based on the similarity of their annotations. We model AnnSim as a 1-1 maximum weight bipartite match and exploit properties of existing solvers to provide an efficient solution. We empirically study the performance of AnnSim on real-world datasets of drugs and disease associations from clinical trials and relationships between drugs and (genomic) targets. Using baselines that include a variety of measures, we identify where AnnSim can provide a deeper understanding of the semantics underlying the relatedness of a pair of entities or where it could lead to predicting new links or identifying potential novel patterns. Although AnnSim does not exploit knowledge or properties of a particular domain, its performance compares well with a variety of state-of-the-art domain-specific measures. Database URL: http://www.yeastgenome.org/ © The Author(s) 2015. Published by Oxford University Press.

Discovering gene annotations in biomedical text databases

PubMed Central

Cakmak, Ali; Ozsoyoglu, Gultekin

2008-01-01

Background Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. Results In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO) concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. Conclusion GEANN is useful for two distinct purposes: (i) automating the annotation of genomic entities with Gene Ontology concepts, and (ii) providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate pattern occurrences with similar semantics. Relatively low recall performance of our pattern-based approach may be enhanced either by employing a probabilistic annotation framework based on the annotation neighbourhoods in textual data, or, alternatively, the statistical enrichment threshold may be adjusted to lower values for applications that put more value on achieving higher recall values. PMID:18325104

Discovering gene annotations in biomedical text databases.

PubMed

Cakmak, Ali; Ozsoyoglu, Gultekin

2008-03-06

Genes and gene products are frequently annotated with Gene Ontology concepts based on the evidence provided in genomics articles. Manually locating and curating information about a genomic entity from the biomedical literature requires vast amounts of human effort. Hence, there is clearly a need forautomated computational tools to annotate the genes and gene products with Gene Ontology concepts by computationally capturing the related knowledge embedded in textual data. In this article, we present an automated genomic entity annotation system, GEANN, which extracts information about the characteristics of genes and gene products in article abstracts from PubMed, and translates the discoveredknowledge into Gene Ontology (GO) concepts, a widely-used standardized vocabulary of genomic traits. GEANN utilizes textual "extraction patterns", and a semantic matching framework to locate phrases matching to a pattern and produce Gene Ontology annotations for genes and gene products. In our experiments, GEANN has reached to the precision level of 78% at therecall level of 61%. On a select set of Gene Ontology concepts, GEANN either outperforms or is comparable to two other automated annotation studies. Use of WordNet for semantic pattern matching improves the precision and recall by 24% and 15%, respectively, and the improvement due to semantic pattern matching becomes more apparent as the Gene Ontology terms become more general. GEANN is useful for two distinct purposes: (i) automating the annotation of genomic entities with Gene Ontology concepts, and (ii) providing existing annotations with additional "evidence articles" from the literature. The use of textual extraction patterns that are constructed based on the existing annotations achieve high precision. The semantic pattern matching framework provides a more flexible pattern matching scheme with respect to "exactmatching" with the advantage of locating approximate pattern occurrences with similar semantics. Relatively low recall performance of our pattern-based approach may be enhanced either by employing a probabilistic annotation framework based on the annotation neighbourhoods in textual data, or, alternatively, the statistical enrichment threshold may be adjusted to lower values for applications that put more value on achieving higher recall values.

Video Salient Object Detection via Fully Convolutional Networks.

PubMed

Wang, Wenguan; Shen, Jianbing; Shao, Ling

This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: 1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data and 2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further propose a novel data augmentation technique that simulates video training data from existing annotated image data sets, which enables our network to learn diverse saliency information and prevents overfitting with the limited number of training videos. Leveraging our synthetic video data (150K video sequences) and real videos, our deep video saliency model successfully learns both spatial and temporal saliency cues, thus producing accurate spatiotemporal saliency estimate. We advance the state-of-the-art on the densely annotated video segmentation data set (MAE of .06) and the Freiburg-Berkeley Motion Segmentation data set (MAE of .07), and do so with much improved speed (2 fps with all steps).This paper proposes a deep learning model to efficiently detect salient regions in videos. It addresses two important issues: 1) deep video saliency model training with the absence of sufficiently large and pixel-wise annotated video data and 2) fast video saliency training and detection. The proposed deep video saliency network consists of two modules, for capturing the spatial and temporal saliency information, respectively. The dynamic saliency model, explicitly incorporating saliency estimates from the static saliency model, directly produces spatiotemporal saliency inference without time-consuming optical flow computation. We further propose a novel data augmentation technique that simulates video training data from existing annotated image data sets, which enables our network to learn diverse saliency information and prevents overfitting with the limited number of training videos. Leveraging our synthetic video data (150K video sequences) and real videos, our deep video saliency model successfully learns both spatial and temporal saliency cues, thus producing accurate spatiotemporal saliency estimate. We advance the state-of-the-art on the densely annotated video segmentation data set (MAE of .06) and the Freiburg-Berkeley Motion Segmentation data set (MAE of .07), and do so with much improved speed (2 fps with all steps).

Marital Biography, Social Security Receipt, and Poverty.

PubMed

Lin, I-Fen; Brown, Susan L; Hammersmith, Anna M

2017-01-01

Increasingly, older adults are unmarried, which could mean a larger share is at risk of economic disadvantage. Using data from the 2010 Health and Retirement Study, we chart the diverse range of marital biographies, capturing marital sequences and timing, of adults who are age eligible for Social Security and examine three indicators of economic well-being: Social Security receipt, Social Security benefit levels, and poverty status. Partnereds are disproportionately likely to receive Social Security and they enjoy relatively high Social Security benefits and very low poverty levels. Among singles, economic well-being varies by marital biography and gender. Gray divorced and never-married women face considerable economic insecurity. Their Social Security benefits are relatively low, and their poverty rates are quite high (over 25%), indicating Social Security alone is not sufficient to prevent these women from falling into poverty. By comparison, gray widoweds are the most advantaged singles.

Marital Biography, Social Security Receipt, and Poverty

PubMed Central

Lin, I-Fen; Brown, Susan L.; Hammersmith, Anna M.

2017-01-01

Increasingly, older adults are unmarried, which could mean a larger share is at risk of economic disadvantage. Using data from the 2010 Health and Retirement Study, we chart the diverse range of marital biographies, capturing marital sequences and timing, of adults who are age eligible for Social Security and examine three indicators of economic well-being: Social Security receipt, Social Security benefit levels, and poverty status. Partnereds are disproportionately likely to receive Social Security and they enjoy relatively high Social Security benefits and very low poverty levels. Among singles, economic well-being varies by marital biography and gender. Gray divorced and never-married women face considerable economic insecurity. Their Social Security benefits are relatively low, and their poverty rates are quite high (over 25%), indicating Social Security alone is not sufficient to prevent these women from falling into poverty. By comparison, gray widoweds are the most advantaged singles. PMID:28181867

A comparative analysis of exome capture.

PubMed

Parla, Jennifer S; Iossifov, Ivan; Grabill, Ian; Spector, Mona S; Kramer, Melissa; McCombie, W Richard

2011-09-29

Human exome resequencing using commercial target capture kits has been and is being used for sequencing large numbers of individuals to search for variants associated with various human diseases. We rigorously evaluated the capabilities of two solution exome capture kits. These analyses help clarify the strengths and limitations of those data as well as systematically identify variables that should be considered in the use of those data. Each exome kit performed well at capturing the targets they were designed to capture, which mainly corresponds to the consensus coding sequences (CCDS) annotations of the human genome. In addition, based on their respective targets, each capture kit coupled with high coverage Illumina sequencing produced highly accurate nucleotide calls. However, other databases, such as the Reference Sequence collection (RefSeq), define the exome more broadly, and so not surprisingly, the exome kits did not capture these additional regions. Commercial exome capture kits provide a very efficient way to sequence select areas of the genome at very high accuracy. Here we provide the data to help guide critical analyses of sequencing data derived from these products.

The "Intelligent Classroom": Changing Teaching and Learning with an Evolving Technological Environment.

ERIC Educational Resources Information Center

Winer, Laura R.; Cooperstock, Jeremy

2002-01-01

Describes the development and use of the Intelligent Classroom collaborative project at McGill University that explored technology use to improve teaching and learning. Explains the hardware and software installation that allows for the automated capture of audio, video, slides, and handwritten annotations during a live lecture, with subsequent…

BisQue: cloud-based system for management, annotation, visualization, analysis and data mining of underwater and remote sensing imagery

NASA Astrophysics Data System (ADS)

Fedorov, D.; Miller, R. J.; Kvilekval, K. G.; Doheny, B.; Sampson, S.; Manjunath, B. S.

2016-02-01

Logistical and financial limitations of underwater operations are inherent in marine science, including biodiversity observation. Imagery is a promising way to address these challenges, but the diversity of organisms thwarts simple automated analysis. Recent developments in computer vision methods, such as convolutional neural networks (CNN), are promising for automated classification and detection tasks but are typically very computationally expensive and require extensive training on large datasets. Therefore, managing and connecting distributed computation, large storage and human annotations of diverse marine datasets is crucial for effective application of these methods. BisQue is a cloud-based system for management, annotation, visualization, analysis and data mining of underwater and remote sensing imagery and associated data. Designed to hide the complexity of distributed storage, large computational clusters, diversity of data formats and inhomogeneous computational environments behind a user friendly web-based interface, BisQue is built around an idea of flexible and hierarchical annotations defined by the user. Such textual and graphical annotations can describe captured attributes and the relationships between data elements. Annotations are powerful enough to describe cells in fluorescent 4D images, fish species in underwater videos and kelp beds in aerial imagery. Presently we are developing BisQue-based analysis modules for automated identification of benthic marine organisms. Recent experiments with drop-out and CNN based classification of several thousand annotated underwater images demonstrated an overall accuracy above 70% for the 15 best performing species and above 85% for the top 5 species. Based on these promising results, we have extended bisque with a CNN-based classification system allowing continuous training on user-provided data.

Compositional mining of multiple object API protocols through state abstraction.

PubMed

Dai, Ziying; Mao, Xiaoguang; Lei, Yan; Qi, Yuhua; Wang, Rui; Gu, Bin

2013-01-01

API protocols specify correct sequences of method invocations. Despite their usefulness, API protocols are often unavailable in practice because writing them is cumbersome and error prone. Multiple object API protocols are more expressive than single object API protocols. However, the huge number of objects of typical object-oriented programs poses a major challenge to the automatic mining of multiple object API protocols: besides maintaining scalability, it is important to capture various object interactions. Current approaches utilize various heuristics to focus on small sets of methods. In this paper, we present a general, scalable, multiple object API protocols mining approach that can capture all object interactions. Our approach uses abstract field values to label object states during the mining process. We first mine single object typestates as finite state automata whose transitions are annotated with states of interacting objects before and after the execution of the corresponding method and then construct multiple object API protocols by composing these annotated single object typestates. We implement our approach for Java and evaluate it through a series of experiments.

Compositional Mining of Multiple Object API Protocols through State Abstraction

PubMed Central

Mao, Xiaoguang; Qi, Yuhua; Wang, Rui; Gu, Bin

2013-01-01

API protocols specify correct sequences of method invocations. Despite their usefulness, API protocols are often unavailable in practice because writing them is cumbersome and error prone. Multiple object API protocols are more expressive than single object API protocols. However, the huge number of objects of typical object-oriented programs poses a major challenge to the automatic mining of multiple object API protocols: besides maintaining scalability, it is important to capture various object interactions. Current approaches utilize various heuristics to focus on small sets of methods. In this paper, we present a general, scalable, multiple object API protocols mining approach that can capture all object interactions. Our approach uses abstract field values to label object states during the mining process. We first mine single object typestates as finite state automata whose transitions are annotated with states of interacting objects before and after the execution of the corresponding method and then construct multiple object API protocols by composing these annotated single object typestates. We implement our approach for Java and evaluate it through a series of experiments. PMID:23844378

Initial sequence and comparative analysis of the cat genome

PubMed Central

Pontius, Joan U.; Mullikin, James C.; Smith, Douglas R.; Lindblad-Toh, Kerstin; Gnerre, Sante; Clamp, Michele; Chang, Jean; Stephens, Robert; Neelam, Beena; Volfovsky, Natalia; Schäffer, Alejandro A.; Agarwala, Richa; Narfström, Kristina; Murphy, William J.; Giger, Urs; Roca, Alfred L.; Antunes, Agostinho; Menotti-Raymond, Marilyn; Yuhki, Naoya; Pecon-Slattery, Jill; Johnson, Warren E.; Bourque, Guillaume; Tesler, Glenn; O’Brien, Stephen J.

2007-01-01

The genome sequence (1.9-fold coverage) of an inbred Abyssinian domestic cat was assembled, mapped, and annotated with a comparative approach that involved cross-reference to annotated genome assemblies of six mammals (human, chimpanzee, mouse, rat, dog, and cow). The results resolved chromosomal positions for 663,480 contigs, 20,285 putative feline gene orthologs, and 133,499 conserved sequence blocks (CSBs). Additional annotated features include repetitive elements, endogenous retroviral sequences, nuclear mitochondrial (numt) sequences, micro-RNAs, and evolutionary breakpoints that suggest historic balancing of translocation and inversion incidences in distinct mammalian lineages. Large numbers of single nucleotide polymorphisms (SNPs), deletion insertion polymorphisms (DIPs), and short tandem repeats (STRs), suitable for linkage or association studies were characterized in the context of long stretches of chromosome homozygosity. In spite of the light coverage capturing ∼65% of euchromatin sequence from the cat genome, these comparative insights shed new light on the tempo and mode of gene/genome evolution in mammals, promise several research applications for the cat, and also illustrate that a comparative approach using more deeply covered mammals provides an informative, preliminary annotation of a light (1.9-fold) coverage mammal genome sequence. PMID:17975172

The history of the CATH structural classification of protein domains.

PubMed

Sillitoe, Ian; Dawson, Natalie; Thornton, Janet; Orengo, Christine

2015-12-01

This article presents a historical review of the protein structure classification database CATH. Together with the SCOP database, CATH remains comprehensive and reasonably up-to-date with the now more than 100,000 protein structures in the PDB. We review the expansion of the CATH and SCOP resources to capture predicted domain structures in the genome sequence data and to provide information on the likely functions of proteins mediated by their constituent domains. The establishment of comprehensive function annotation resources has also meant that domain families can be functionally annotated allowing insights into functional divergence and evolution within protein families. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

Performance and Architecture Lab Modeling Tool

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

2014-06-19

Analytical application performance models are critical for diagnosing performance-limiting resources, optimizing systems, and designing machines. Creating models, however, is difficult. Furthermore, models are frequently expressed in forms that are hard to distribute and validate. The Performance and Architecture Lab Modeling tool, or Palm, is a modeling tool designed to make application modeling easier. Palm provides a source code modeling annotation language. Not only does the modeling language divide the modeling task into sub problems, it formally links an application's source code with its model. This link is important because a model's purpose is to capture application behavior. Furthermore, this linkmore » makes it possible to define rules for generating models according to source code organization. Palm generates hierarchical models according to well-defined rules. Given an application, a set of annotations, and a representative execution environment, Palm will generate the same model. A generated model is a an executable program whose constituent parts directly correspond to the modeled application. Palm generates models by combining top-down (human-provided) semantic insight with bottom-up static and dynamic analysis. A model's hierarchy is defined by static and dynamic source code structure. Because Palm coordinates models and source code, Palm's models are 'first-class' and reproducible. Palm automates common modeling tasks. For instance, Palm incorporates measurements to focus attention, represent constant behavior, and validate models. Palm's workflow is as follows. The workflow's input is source code annotated with Palm modeling annotations. The most important annotation models an instance of a block of code. Given annotated source code, the Palm Compiler produces executables and the Palm Monitor collects a representative performance profile. The Palm Generator synthesizes a model based on the static and dynamic mapping of annotations to program behavior. The model -- an executable program -- is a hierarchical composition of annotation functions, synthesized functions, statistics for runtime values, and performance measurements.« less

Boosting drug named entity recognition using an aggregate classifier.

PubMed

Korkontzelos, Ioannis; Piliouras, Dimitrios; Dowsey, Andrew W; Ananiadou, Sophia

2015-10-01

Drug named entity recognition (NER) is a critical step for complex biomedical NLP tasks such as the extraction of pharmacogenomic, pharmacodynamic and pharmacokinetic parameters. Large quantities of high quality training data are almost always a prerequisite for employing supervised machine-learning techniques to achieve high classification performance. However, the human labour needed to produce and maintain such resources is a significant limitation. In this study, we improve the performance of drug NER without relying exclusively on manual annotations. We perform drug NER using either a small gold-standard corpus (120 abstracts) or no corpus at all. In our approach, we develop a voting system to combine a number of heterogeneous models, based on dictionary knowledge, gold-standard corpora and silver annotations, to enhance performance. To improve recall, we employed genetic programming to evolve 11 regular-expression patterns that capture common drug suffixes and used them as an extra means for recognition. Our approach uses a dictionary of drug names, i.e. DrugBank, a small manually annotated corpus, i.e. the pharmacokinetic corpus, and a part of the UKPMC database, as raw biomedical text. Gold-standard and silver annotated data are used to train maximum entropy and multinomial logistic regression classifiers. Aggregating drug NER methods, based on gold-standard annotations, dictionary knowledge and patterns, improved the performance on models trained on gold-standard annotations, only, achieving a maximum F-score of 95%. In addition, combining models trained on silver annotations, dictionary knowledge and patterns are shown to achieve comparable performance to models trained exclusively on gold-standard data. The main reason appears to be the morphological similarities shared among drug names. We conclude that gold-standard data are not a hard requirement for drug NER. Combining heterogeneous models build on dictionary knowledge can achieve similar or comparable classification performance with that of the best performing model trained on gold-standard annotations. Copyright © 2015 The Authors. Published by Elsevier B.V. All rights reserved.

The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation model.

PubMed

Mongkolwat, Pattanasak; Kleper, Vladimir; Talbot, Skip; Rubin, Daniel

2014-12-01

Knowledge contained within in vivo imaging annotated by human experts or computer programs is typically stored as unstructured text and separated from other associated information. The National Cancer Informatics Program (NCIP) Annotation and Image Markup (AIM) Foundation information model is an evolution of the National Institute of Health's (NIH) National Cancer Institute's (NCI) Cancer Bioinformatics Grid (caBIG®) AIM model. The model applies to various image types created by various techniques and disciplines. It has evolved in response to the feedback and changing demands from the imaging community at NCI. The foundation model serves as a base for other imaging disciplines that want to extend the type of information the model collects. The model captures physical entities and their characteristics, imaging observation entities and their characteristics, markups (two- and three-dimensional), AIM statements, calculations, image source, inferences, annotation role, task context or workflow, audit trail, AIM creator details, equipment used to create AIM instances, subject demographics, and adjudication observations. An AIM instance can be stored as a Digital Imaging and Communications in Medicine (DICOM) structured reporting (SR) object or Extensible Markup Language (XML) document for further processing and analysis. An AIM instance consists of one or more annotations and associated markups of a single finding along with other ancillary information in the AIM model. An annotation describes information about the meaning of pixel data in an image. A markup is a graphical drawing placed on the image that depicts a region of interest. This paper describes fundamental AIM concepts and how to use and extend AIM for various imaging disciplines.

The center for expanded data annotation and retrieval

PubMed Central

Bean, Carol A; Cheung, Kei-Hoi; Dumontier, Michel; Durante, Kim A; Gevaert, Olivier; Gonzalez-Beltran, Alejandra; Khatri, Purvesh; Kleinstein, Steven H; O’Connor, Martin J; Pouliot, Yannick; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Wiser, Jeffrey A

2015-01-01

The Center for Expanded Data Annotation and Retrieval is studying the creation of comprehensive and expressive metadata for biomedical datasets to facilitate data discovery, data interpretation, and data reuse. We take advantage of emerging community-based standard templates for describing different kinds of biomedical datasets, and we investigate the use of computational techniques to help investigators to assemble templates and to fill in their values. We are creating a repository of metadata from which we plan to identify metadata patterns that will drive predictive data entry when filling in metadata templates. The metadata repository not only will capture annotations specified when experimental datasets are initially created, but also will incorporate links to the published literature, including secondary analyses and possible refinements or retractions of experimental interpretations. By working initially with the Human Immunology Project Consortium and the developers of the ImmPort data repository, we are developing and evaluating an end-to-end solution to the problems of metadata authoring and management that will generalize to other data-management environments. PMID:26112029

An Annotation Agnostic Algorithm for Detecting Nascent RNA Transcripts in GRO-Seq.

PubMed

Azofeifa, Joseph G; Allen, Mary A; Lladser, Manuel E; Dowell, Robin D

2017-01-01

We present a fast and simple algorithm to detect nascent RNA transcription in global nuclear run-on sequencing (GRO-seq). GRO-seq is a relatively new protocol that captures nascent transcripts from actively engaged polymerase, providing a direct read-out on bona fide transcription. Most traditional assays, such as RNA-seq, measure steady state RNA levels which are affected by transcription, post-transcriptional processing, and RNA stability. GRO-seq data, however, presents unique analysis challenges that are only beginning to be addressed. Here, we describe a new algorithm, Fast Read Stitcher (FStitch), that takes advantage of two popular machine-learning techniques, hidden Markov models and logistic regression, to classify which regions of the genome are transcribed. Given a small user-defined training set, our algorithm is accurate, robust to varying read depth, annotation agnostic, and fast. Analysis of GRO-seq data without a priori need for annotation uncovers surprising new insights into several aspects of the transcription process.

Phage phenomics: Physiological approaches to characterize novel viral proteins

ScienceCinema

Sanchez, Savannah E. [San Diego State Univ., San Diego, CA (United States); Cuevas, Daniel A. [San Diego State Univ., San Diego, CA (United States); Rostron, Jason E. [San Diego State Univ., San Diego, CA (United States); Liang, Tiffany Y. [San Diego State Univ., San Diego, CA (United States); Pivaroff, Cullen G. [San Diego State Univ., San Diego, CA (United States); Haynes, Matthew R. [San Diego State Univ., San Diego, CA (United States); Nulton, Jim [San Diego State Univ., San Diego, CA (United States); Felts, Ben [San Diego State Univ., San Diego, CA (United States); Bailey, Barbara A. [San Diego State Univ., San Diego, CA (United States); Salamon, Peter [San Diego State Univ., San Diego, CA (United States); Edwards, Robert A. [San Diego State Univ., San Diego, CA (United States); Argonne National Lab. (ANL), Argonne, IL (United States); Burgin, Alex B. [Broad Institute, Cambridge, MA (United States); Segall, Anca M. [San Diego State Univ., San Diego, CA (United States); Rohwer, Forest [San Diego State Univ., San Diego, CA (United States)

2018-06-21

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysis by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.

PubSearch and PubFetch: a simple management system for semiautomated retrieval and annotation of biological information from the literature.

PubMed

Yoo, Danny; Xu, Iris; Berardini, Tanya Z; Rhee, Seung Yon; Narayanasamy, Vijay; Twigger, Simon

2006-03-01

For most systems in biology, a large body of literature exists that describes the complexity of the system based on experimental results. Manual review of this literature to extract targeted information into biological databases is difficult and time consuming. To address this problem, we developed PubSearch and PubFetch, which store literature, keyword, and gene information in a relational database, index the literature with keywords and gene names, and provide a Web user interface for annotating the genes from experimental data found in the associated literature. A set of protocols is provided in this unit for installing, populating, running, and using PubSearch and PubFetch. In addition, we provide support protocols for performing controlled vocabulary annotations. Intended users of PubSearch and PubFetch are database curators and biology researchers interested in tracking the literature and capturing information about genes of interest in a more effective way than with conventional spreadsheets and lab notebooks.

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

Sanchez, Savannah E.; Cuevas, Daniel A.; Rostron, Jason E.

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysismore » by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.« less

Enabling a Community to Dissect an Organism: Overview of the Neurospora Functional Genomics Project

PubMed Central

Dunlap, Jay C.; Borkovich, Katherine A.; Henn, Matthew R.; Turner, Gloria E.; Sachs, Matthew S.; Glass, N. Louise; McCluskey, Kevin; Plamann, Michael; Galagan, James E.; Birren, Bruce W.; Weiss, Richard L.; Townsend, Jeffrey P.; Loros, Jennifer J.; Nelson, Mary Anne; Lambreghts, Randy; Colot, Hildur V.; Park, Gyungsoon; Collopy, Patrick; Ringelberg, Carol; Crew, Christopher; Litvinkova, Liubov; DeCaprio, Dave; Hood, Heather M.; Curilla, Susan; Shi, Mi; Crawford, Matthew; Koerhsen, Michael; Montgomery, Phil; Larson, Lisa; Pearson, Matthew; Kasuga, Takao; Tian, Chaoguang; Baştürkmen, Meray; Altamirano, Lorena; Xu, Junhuan

2013-01-01

A consortium of investigators is engaged in a functional genomics project centered on the filamentous fungus Neurospora, with an eye to opening up the functional genomic analysis of all the filamentous fungi. The overall goal of the four interdependent projects in this effort is to acccomplish functional genomics, annotation, and expression analyses of Neurospora crassa, a filamentous fungus that is an established model for the assemblage of over 250,000 species of nonyeast fungi. Building from the completely sequenced 43-Mb Neurospora genome, Project 1 is pursuing the systematic disruption of genes through targeted gene replacements, phenotypic analysis of mutant strains, and their distribution to the scientific community at large. Project 2, through a primary focus in Annotation and Bioinformatics, has developed a platform for electronically capturing community feedback and data about the existing annotation, while building and maintaining a database to capture and display information about phenotypes. Oligonucleotide-based microarrays created in Project 3 are being used to collect baseline expression data for the nearly 11,000 distinguishable transcripts in Neurospora under various conditions of growth and development, and eventually to begin to analyze the global effects of loss of novel genes in strains created by Project 1. cDNA libraries generated in Project 4 document the overall complexity of expressed sequences in Neurospora, including alternative splicing alternative promoters and antisense transcripts. In addition, these studies have driven the assembly of an SNP map presently populated by nearly 300 markers that will greatly accelerate the positional cloning of genes. PMID:17352902

EuroPhenome: a repository for high-throughput mouse phenotyping data

PubMed Central

Morgan, Hugh; Beck, Tim; Blake, Andrew; Gates, Hilary; Adams, Niels; Debouzy, Guillaume; Leblanc, Sophie; Lengger, Christoph; Maier, Holger; Melvin, David; Meziane, Hamid; Richardson, Dave; Wells, Sara; White, Jacqui; Wood, Joe; de Angelis, Martin Hrabé; Brown, Steve D. M.; Hancock, John M.; Mallon, Ann-Marie

2010-01-01

The broad aim of biomedical science in the postgenomic era is to link genomic and phenotype information to allow deeper understanding of the processes leading from genomic changes to altered phenotype and disease. The EuroPhenome project (http://www.EuroPhenome.org) is a comprehensive resource for raw and annotated high-throughput phenotyping data arising from projects such as EUMODIC. EUMODIC is gathering data from the EMPReSSslim pipeline (http://www.empress.har.mrc.ac.uk/) which is performed on inbred mouse strains and knock-out lines arising from the EUCOMM project. The EuroPhenome interface allows the user to access the data via the phenotype or genotype. It also allows the user to access the data in a variety of ways, including graphical display, statistical analysis and access to the raw data via web services. The raw phenotyping data captured in EuroPhenome is annotated by an annotation pipeline which automatically identifies statistically different mutants from the appropriate baseline and assigns ontology terms for that specific test. Mutant phenotypes can be quickly identified using two EuroPhenome tools: PhenoMap, a graphical representation of statistically relevant phenotypes, and mining for a mutant using ontology terms. To assist with data definition and cross-database comparisons, phenotype data is annotated using combinations of terms from biological ontologies. PMID:19933761

Time series modeling of live-cell shape dynamics for image-based phenotypic profiling.

PubMed

Gordonov, Simon; Hwang, Mun Kyung; Wells, Alan; Gertler, Frank B; Lauffenburger, Douglas A; Bathe, Mark

2016-01-01

Live-cell imaging can be used to capture spatio-temporal aspects of cellular responses that are not accessible to fixed-cell imaging. As the use of live-cell imaging continues to increase, new computational procedures are needed to characterize and classify the temporal dynamics of individual cells. For this purpose, here we present the general experimental-computational framework SAPHIRE (Stochastic Annotation of Phenotypic Individual-cell Responses) to characterize phenotypic cellular responses from time series imaging datasets. Hidden Markov modeling is used to infer and annotate morphological state and state-switching properties from image-derived cell shape measurements. Time series modeling is performed on each cell individually, making the approach broadly useful for analyzing asynchronous cell populations. Two-color fluorescent cells simultaneously expressing actin and nuclear reporters enabled us to profile temporal changes in cell shape following pharmacological inhibition of cytoskeleton-regulatory signaling pathways. Results are compared with existing approaches conventionally applied to fixed-cell imaging datasets, and indicate that time series modeling captures heterogeneous dynamic cellular responses that can improve drug classification and offer additional important insight into mechanisms of drug action. The software is available at http://saphire-hcs.org.

Quantifying human-environment interactions using videography in the context of infectious disease transmission.

PubMed

Julian, Timothy R; Bustos, Carla; Kwong, Laura H; Badilla, Alejandro D; Lee, Julia; Bischel, Heather N; Canales, Robert A

2018-05-08

Quantitative data on human-environment interactions are needed to fully understand infectious disease transmission processes and conduct accurate risk assessments. Interaction events occur during an individual's movement through, and contact with, the environment, and can be quantified using diverse methodologies. Methods that utilize videography, coupled with specialized software, can provide a permanent record of events, collect detailed interactions in high resolution, be reviewed for accuracy, capture events difficult to observe in real-time, and gather multiple concurrent phenomena. In the accompanying video, the use of specialized software to capture humanenvironment interactions for human exposure and disease transmission is highlighted. Use of videography, combined with specialized software, allows for the collection of accurate quantitative representations of human-environment interactions in high resolution. Two specialized programs include the Virtual Timing Device for the Personal Computer, which collects sequential microlevel activity time series of contact events and interactions, and LiveTrak, which is optimized to facilitate annotation of events in real-time. Opportunities to annotate behaviors at high resolution using these tools are promising, permitting detailed records that can be summarized to gain information on infectious disease transmission and incorporated into more complex models of human exposure and risk.

Dictionary-driven protein annotation.

PubMed

Rigoutsos, Isidore; Huynh, Tien; Floratos, Aris; Parida, Laxmi; Platt, Daniel

2002-09-01

Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous research groups. With the advent of advanced sequencing methods and systems, the number of amino acid sequences that are being deposited in the public databases has been increasing steadily. This has in turn generated a renewed demand for automated approaches that can annotate individual sequences and complete genomes quickly, exhaustively and objectively. In this paper, we present one such approach that is centered around and exploits the Bio-Dictionary, a collection of amino acid patterns that completely covers the natural sequence space and can capture functional and structural signals that have been reused during evolution, within and across protein families. Our annotation approach also makes use of a weighted, position-specific scoring scheme that is unaffected by the over-representation of well-conserved proteins and protein fragments in the databases used. For a given query sequence, the method permits one to determine, in a single pass, the following: local and global similarities between the query and any protein already present in a public database; the likeness of the query to all available archaeal/ bacterial/eukaryotic/viral sequences in the database as a function of amino acid position within the query; the character of secondary structure of the query as a function of amino acid position within the query; the cytoplasmic, transmembrane or extracellular behavior of the query; the nature and position of binding domains, active sites, post-translationally modified sites, signal peptides, etc. In terms of performance, the proposed method is exhaustive, objective and allows for the rapid annotation of individual sequences and full genomes. Annotation examples are presented and discussed in Results, including individual queries and complete genomes that were released publicly after we built the Bio-Dictionary that is used in our experiments. Finally, we have computed the annotations of more than 70 complete genomes and made them available on the World Wide Web at http://cbcsrv.watson.ibm.com/Annotations/.

MSFC Space Station Program Commonly Used Acronyms and Abbreviations Listing

NASA Technical Reports Server (NTRS)

Gates, Thomas G.

1988-01-01

The Marshall Space Flight Center maintains an active history program to assure that the foundation of the Center's history is captured and preserved for current and future generations. As part of that overall effort, the Center began a project in 1987 to capture historical information and documentation on the Marshall Center's roles regarding Space Shuttle and Space Station. This document is MSFC Space Station Program Commonly Used Acronyms and Abbreviations Listing. It contains acronyms and abbreviations used in Space Station documentation and in the Historian Annotated Bibliography of Space Station Program. The information may be used by the researcher as a reference tool.

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

PubMed Central

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

2011-01-01

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

Phage phenomics: Physiological approaches to characterize novel viral proteins

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

Sanchez, Savannah E.; Cuevas, Daniel A.; Rostron, Jason E.

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysismore » by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.« less

Phage phenomics: Physiological approaches to characterize novel viral proteins

DOE PAGES

Sanchez, Savannah E.; Cuevas, Daniel A.; Rostron, Jason E.; ...

2015-06-11

Current investigations into phage-host interactions are dependent on extrapolating knowledge from (meta)genomes. Interestingly, 60 - 95% of all phage sequences share no homology to current annotated proteins. As a result, a large proportion of phage genes are annotated as hypothetical. This reality heavily affects the annotation of both structural and auxiliary metabolic genes. Here we present phenomic methods designed to capture the physiological response(s) of a selected host during expression of one of these unknown phage genes. Multi-phenotype Assay Plates (MAPs) are used to monitor the diversity of host substrate utilization and subsequent biomass formation, while metabolomics provides bi-product analysismore » by monitoring metabolite abundance and diversity. Both tools are used simultaneously to provide a phenotypic profile associated with expression of a single putative phage open reading frame (ORF). Thus, representative results for both methods are compared, highlighting the phenotypic profile differences of a host carrying either putative structural or metabolic phage genes. In addition, the visualization techniques and high throughput computational pipelines that facilitated experimental analysis are presented.« less

Algae from the arid southwestern United States: an annotated bibliography

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

Thomas, W.H.; Gaines, S.R.

Desert algae are attractive biomass producers for capturing solar energy through photosynthesis of organic matter. They are probably capable of higher yields and efficiencies of light utilization than higher plants, and are already adapted to extremes of sunlight intensity, salinity and temperature such as are found in the desert. This report consists of an annotated bibliography of the literature on algae from the arid southwestern United States. It was prepared in anticipation of efforts to isolate desert algae and study their yields in the laboratory. These steps are necessary prior to setting up outdoor algal culture ponds. Desert areas aremore » attractive for such applications because land, sunlight, and, to some extent, water resources are abundant there. References are sorted by state.« less

Integrated data management for clinical studies: automatic transformation of data models with semantic annotations for principal investigators, data managers and statisticians.

PubMed

Dugas, Martin; Dugas-Breit, Susanne

2014-01-01

Design, execution and analysis of clinical studies involves several stakeholders with different professional backgrounds. Typically, principle investigators are familiar with standard office tools, data managers apply electronic data capture (EDC) systems and statisticians work with statistics software. Case report forms (CRFs) specify the data model of study subjects, evolve over time and consist of hundreds to thousands of data items per study. To avoid erroneous manual transformation work, a converting tool for different representations of study data models was designed. It can convert between office format, EDC and statistics format. In addition, it supports semantic annotations, which enable precise definitions for data items. A reference implementation is available as open source package ODMconverter at http://cran.r-project.org.

Mycobacteriophage genome database.

PubMed

Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

2011-01-01

Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

Screen-Capturing System with Two-Layer Display for PowerPoint Presentation to Enhance Classroom Education

ERIC Educational Resources Information Center

Lai, Yen-Shou; Tsai, Hung-Hsu; Yu, Pao-Ta

2011-01-01

This paper proposes a new presentation system integrating a Microsoft PowerPoint presentation in a two-layer method, called the TL system, to promote learning in a physical classroom. With the TL system, teachers can readily control hints or annotations as a way of making them visible or invisible to students so as to reduce information load. In…

A Digital Approach to Learning Petrology

NASA Astrophysics Data System (ADS)

Reid, M. R.

2011-12-01

In the undergraduate igneous and metamorphic petrology course at Northern Arizona University, we are employing petrographic microscopes equipped with relatively inexpensive ( $200) digital cameras that are linked to pen-tablet computers. The camera-tablet systems can assist student learning in a variety of ways. Images provided by the tablet computers can be used for helping students filter the visually complex specimens they examine. Instructors and students can simultaneously view the same petrographic features captured by the cameras and exchange information about them by pointing to salient features using the tablet pen. These images can become part of a virtual mineral/rock/texture portfolio tailored to individual student's needs. Captured digital illustrations can be annotated with digital ink or computer graphics tools; this activity emulates essential features of more traditional line drawings (visualizing an appropriate feature and selecting a representative image of it, internalizing the feature through studying and annotating it) while minimizing the frustration that many students feel about drawing. In these ways, we aim to help a student progress more efficiently from novice to expert. A number of our petrology laboratory exercises involve use of the camera-tablet systems for collaborative learning. Observational responsibilities are distributed among individual members of teams in order to increase interdependence and accountability, and to encourage efficiency. Annotated digital images are used to share students' findings and arrive at an understanding of an entire rock suite. This interdependence increases the individual's sense of responsibility for their work, and reporting out encourages students to practice use of technical vocabulary and to defend their observations. Pre- and post-course student interest in the camera-tablet systems has been assessed. In a post-course survey, the majority of students reported that, if available, they would use camera-tablet systems to capture microscope images (77%) and to make notes on images (71%). An informal focus group recommended introducing the cameras as soon as possible and having them available for making personal mineralogy/petrology portfolios. Because the stakes are perceived as high, use of the camera-tablet systems for peer-peer learning has been progressively modified to bolster student confidence in their collaborative efforts.

CHiCP: a web-based tool for the integrative and interactive visualization of promoter capture Hi-C datasets.

PubMed

Schofield, E C; Carver, T; Achuthan, P; Freire-Pritchett, P; Spivakov, M; Todd, J A; Burren, O S

2016-08-15

Promoter capture Hi-C (PCHi-C) allows the genome-wide interrogation of physical interactions between distal DNA regulatory elements and gene promoters in multiple tissue contexts. Visual integration of the resultant chromosome interaction maps with other sources of genomic annotations can provide insight into underlying regulatory mechanisms. We have developed Capture HiC Plotter (CHiCP), a web-based tool that allows interactive exploration of PCHi-C interaction maps and integration with both public and user-defined genomic datasets. CHiCP is freely accessible from www.chicp.org and supports most major HTML5 compliant web browsers. Full source code and installation instructions are available from http://github.com/D-I-L/django-chicp ob219@cam.ac.uk. © The Author 2016. Published by Oxford University Press. All rights reserved.

Watch-and-Comment as an Approach to Collaboratively Annotate Points of Interest in Video and Interactive-TV Programs

NASA Astrophysics Data System (ADS)

Pimentel, Maria Da Graça C.; Cattelan, Renan G.; Melo, Erick L.; Freitas, Giliard B.; Teixeira, Cesar A.

In earlier work we proposed the Watch-and-Comment (WaC) paradigm as the seamless capture of multimodal comments made by one or more users while watching a video, resulting in the automatic generation of multimedia documents specifying annotated interactive videos. The aim is to allow services to be offered by applying document engineering techniques to the multimedia document generated automatically. The WaC paradigm was demonstrated with a WaCTool prototype application which supports multimodal annotation over video frames and segments, producing a corresponding interactive video. In this chapter, we extend the WaC paradigm to consider contexts in which several viewers may use their own mobile devices while watching and commenting on an interactive-TV program. We first review our previous work. Next, we discuss scenarios in which mobile users can collaborate via the WaC paradigm. We then present a new prototype application which allows users to employ their mobile devices to collaboratively annotate points of interest in video and interactive-TV programs. We also detail the current software infrastructure which supports our new prototype; the infrastructure extends the Ginga middleware for the Brazilian Digital TV with an implementation of the UPnP protocol - the aim is to provide the seamless integration of the users' mobile devices into the TV environment. As a result, the work reported in this chapter defines the WaC paradigm for the mobile-user as an approach to allow the collaborative annotation of the points of interest in video and interactive-TV programs.

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

PubMed

Slenter, Denise N; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M T; Evelo, Chris T; Pico, Alexander R; Willighagen, Egon L

2018-01-04

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

An Augmented Reality-Based Approach for Surgical Telementoring in Austere Environments.

PubMed

Andersen, Dan; Popescu, Voicu; Cabrera, Maria Eugenia; Shanghavi, Aditya; Mullis, Brian; Marley, Sherri; Gomez, Gerardo; Wachs, Juan P

2017-03-01

Telementoring can improve treatment of combat trauma injuries by connecting remote experienced surgeons with local less-experienced surgeons in an austere environment. Current surgical telementoring systems force the local surgeon to regularly shift focus away from the operating field to receive expert guidance, which can lead to surgery delays or even errors. The System for Telementoring with Augmented Reality (STAR) integrates expert-created annotations directly into the local surgeon's field of view. The local surgeon views the operating field by looking at a tablet display suspended between the patient and the surgeon that captures video of the surgical field. The remote surgeon remotely adds graphical annotations to the video. The annotations are sent back and displayed to the local surgeon while being automatically anchored to the operating field elements they describe. A technical evaluation demonstrates that STAR robustly anchors annotations despite tablet repositioning and occlusions. In a user study, participants used either STAR or a conventional telementoring system to precisely mark locations on a surgical simulator under a remote surgeon's guidance. Participants who used STAR completed the task with fewer focus shifts and with greater accuracy. The STAR reduces the local surgeon's need to shift attention during surgery, allowing him or her to continuously work while looking "through" the tablet screen. Reprint & Copyright © 2017 Association of Military Surgeons of the U.S.

Features of Heart Rate Variability Capture Regulatory Changes During Kangaroo Care in Preterm Infants.

PubMed

Kommers, Deedee R; Joshi, Rohan; van Pul, Carola; Atallah, Louis; Feijs, Loe; Oei, Guid; Bambang Oetomo, Sidarto; Andriessen, Peter

2017-03-01

To determine whether heart rate variability (HRV) can serve as a surrogate measure to track regulatory changes during kangaroo care, a period of parental coregulation distinct from regulation within the incubator. Nurses annotated the starting and ending times of kangaroo care for 3 months. The pre-kangaroo care, during-kangaroo care, and post-kangaroo care data were retrieved in infants with at least 10 accurately annotated kangaroo care sessions. Eight HRV features (5 in the time domain and 3 in the frequency domain) were used to visually and statistically compare the pre-kangaroo care and during-kangaroo care periods. Two of these features, capturing the percentage of heart rate decelerations and the extent of heart rate decelerations, were newly developed for preterm infants. A total of 191 kangaroo care sessions were investigated in 11 preterm infants. Despite clinically irrelevant changes in vital signs, 6 of the 8 HRV features (SD of normal-to-normal intervals, root mean square of the SD, percentage of consecutive normal-to-normal intervals that differ by >50 ms, SD of heart rate decelerations, high-frequency power, and low-frequency/high-frequency ratio) showed a visible and statistically significant difference (P <.01) between stable periods of kangaroo care and pre-kangaroo care. HRV was reduced during kangaroo care owing to a decrease in the extent of transient heart rate decelerations. HRV-based features may be clinically useful for capturing the dynamic changes in autonomic regulation in response to kangaroo care and other changes in environment and state. Copyright © 2016 Elsevier Inc. All rights reserved.

Invertebrates of The H.J. Andrews Experimental Forest, Western Cascades, Oregon: I. An annotated checklist of fleas.

Treesearch

Robert E. Lewis; Chris Maser

1981-01-01

During a trapping survey of small mammals (approximately 3,000 individuals), species of fleas (1,632 specimens) were collected in the H.J. Andrews Experimental Forest, Western Cascades, Oregon. Host mammals were represented by 15 species—6 insectivores and 9 rodents captured from June through September. The collections extend our knowledge of the fauna of Oregon.

SimCheck: An Expressive Type System for Simulink

NASA Technical Reports Server (NTRS)

Roy, Pritam; Shankar, Natarajan

2010-01-01

MATLAB Simulink is a member of a class of visual languages that are used for modeling and simulating physical and cyber-physical systems. A Simulink model consists of blocks with input and output ports connected using links that carry signals. We extend the type system of Simulink with annotations and dimensions/units associated with ports and links. These types can capture invariants on signals as well as relations between signals. We define a type-checker that checks the wellformedness of Simulink blocks with respect to these type annotations. The type checker generates proof obligations that are solved by SRI's Yices solver for satisfiability modulo theories (SMT). This translation can be used to detect type errors, demonstrate counterexamples, generate test cases, or prove the absence of type errors. Our work is an initial step toward the symbolic analysis of MATLAB Simulink models.

LEARNING SEMANTICS-ENHANCED LANGUAGE MODELS APPLIED TO UNSUEPRVISED WSD

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

VERSPOOR, KARIN; LIN, SHOU-DE

An N-gram language model aims at capturing statistical syntactic word order information from corpora. Although the concept of language models has been applied extensively to handle a variety of NLP problems with reasonable success, the standard model does not incorporate semantic information, and consequently limits its applicability to semantic problems such as word sense disambiguation. We propose a framework that integrates semantic information into the language model schema, allowing a system to exploit both syntactic and semantic information to address NLP problems. Furthermore, acknowledging the limited availability of semantically annotated data, we discuss how the proposed model can be learnedmore » without annotated training examples. Finally, we report on a case study showing how the semantics-enhanced language model can be applied to unsupervised word sense disambiguation with promising results.« less

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases.

PubMed

Bagewadi, Shweta; Adhikari, Subash; Dhrangadhariya, Anjani; Irin, Afroza Khanam; Ebeling, Christian; Namasivayam, Aishwarya Alex; Page, Matthew; Hofmann-Apitius, Martin; Senger, Philipp

2015-01-01

Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article's supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer's disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html. © The Author(s) 2015. Published by Oxford University Press.

NeuroTransDB: highly curated and structured transcriptomic metadata for neurodegenerative diseases

PubMed Central

Bagewadi, Shweta; Adhikari, Subash; Dhrangadhariya, Anjani; Irin, Afroza Khanam; Ebeling, Christian; Namasivayam, Aishwarya Alex; Page, Matthew; Hofmann-Apitius, Martin

2015-01-01

Neurodegenerative diseases are chronic debilitating conditions, characterized by progressive loss of neurons that represent a significant health care burden as the global elderly population continues to grow. Over the past decade, high-throughput technologies such as the Affymetrix GeneChip microarrays have provided new perspectives into the pathomechanisms underlying neurodegeneration. Public transcriptomic data repositories, namely Gene Expression Omnibus and curated ArrayExpress, enable researchers to conduct integrative meta-analysis; increasing the power to detect differentially regulated genes in disease and explore patterns of gene dysregulation across biologically related studies. The reliability of retrospective, large-scale integrative analyses depends on an appropriate combination of related datasets, in turn requiring detailed meta-annotations capturing the experimental setup. In most cases, we observe huge variation in compliance to defined standards for submitted metadata in public databases. Much of the information to complete, or refine meta-annotations are distributed in the associated publications. For example, tissue preparation or comorbidity information is frequently described in an article’s supplementary tables. Several value-added databases have employed additional manual efforts to overcome this limitation. However, none of these databases explicate annotations that distinguish human and animal models in neurodegeneration context. Therefore, adopting a more specific disease focus, in combination with dedicated disease ontologies, will better empower the selection of comparable studies with refined annotations to address the research question at hand. In this article, we describe the detailed development of NeuroTransDB, a manually curated database containing metadata annotations for neurodegenerative studies. The database contains more than 20 dimensions of metadata annotations within 31 mouse, 5 rat and 45 human studies, defined in collaboration with domain disease experts. We elucidate the step-by-step guidelines used to critically prioritize studies from public archives and their metadata curation and discuss the key challenges encountered. Curated metadata for Alzheimer’s disease gene expression studies are available for download. Database URL: www.scai.fraunhofer.de/NeuroTransDB.html PMID:26475471

Dictionary-driven protein annotation

PubMed Central

Rigoutsos, Isidore; Huynh, Tien; Floratos, Aris; Parida, Laxmi; Platt, Daniel

2002-01-01

Computational methods seeking to automatically determine the properties (functional, structural, physicochemical, etc.) of a protein directly from the sequence have long been the focus of numerous research groups. With the advent of advanced sequencing methods and systems, the number of amino acid sequences that are being deposited in the public databases has been increasing steadily. This has in turn generated a renewed demand for automated approaches that can annotate individual sequences and complete genomes quickly, exhaustively and objectively. In this paper, we present one such approach that is centered around and exploits the Bio-Dictionary, a collection of amino acid patterns that completely covers the natural sequence space and can capture functional and structural signals that have been reused during evolution, within and across protein families. Our annotation approach also makes use of a weighted, position-specific scoring scheme that is unaffected by the over-representation of well-conserved proteins and protein fragments in the databases used. For a given query sequence, the method permits one to determine, in a single pass, the following: local and global similarities between the query and any protein already present in a public database; the likeness of the query to all available archaeal/bacterial/eukaryotic/viral sequences in the database as a function of amino acid position within the query; the character of secondary structure of the query as a function of amino acid position within the query; the cytoplasmic, transmembrane or extracellular behavior of the query; the nature and position of binding domains, active sites, post-translationally modified sites, signal peptides, etc. In terms of performance, the proposed method is exhaustive, objective and allows for the rapid annotation of individual sequences and full genomes. Annotation examples are presented and discussed in Results, including individual queries and complete genomes that were released publicly after we built the Bio-Dictionary that is used in our experiments. Finally, we have computed the annotations of more than 70 complete genomes and made them available on the World Wide Web at http://cbcsrv.watson.ibm.com/Annotations/. PMID:12202776

Artistic image analysis using graph-based learning approaches.

PubMed

Carneiro, Gustavo

2013-08-01

We introduce a new methodology for the problem of artistic image analysis, which among other tasks, involves the automatic identification of visual classes present in an art work. In this paper, we advocate the idea that artistic image analysis must explore a graph that captures the network of artistic influences by computing the similarities in terms of appearance and manual annotation. One of the novelties of our methodology is the proposed formulation that is a principled way of combining these two similarities in a single graph. Using this graph, we show that an efficient random walk algorithm based on an inverted label propagation formulation produces more accurate annotation and retrieval results compared with the following baseline algorithms: bag of visual words, label propagation, matrix completion, and structural learning. We also show that the proposed approach leads to a more efficient inference and training procedures. This experiment is run on a database containing 988 artistic images (with 49 visual classification problems divided into a multiclass problem with 27 classes and 48 binary problems), where we show the inference and training running times, and quantitative comparisons with respect to several retrieval and annotation performance measures.

Key Provenance of Earth Science Observational Data Products

NASA Astrophysics Data System (ADS)

Conover, H.; Plale, B.; Aktas, M.; Ramachandran, R.; Purohit, P.; Jensen, S.; Graves, S. J.

2011-12-01

As the sheer volume of data increases, particularly evidenced in the earth and environmental sciences, local arrangements for sharing data need to be replaced with reliable records about the what, who, how, and where of a data set or collection. This is frequently called the provenance of a data set. While observational data processing systems in the earth sciences have a long history of capturing metadata about the processing pipeline, current processes are limited in both what is captured and how it is disseminated to the science community. Provenance capture plays a role in scientific data preservation and stewardship precisely because it can automatically capture and represent a coherent picture of the what, how and who of a particular scientific collection. It reflects the transformations that a data collection underwent prior to its current form and the sequence of tasks that were executed and data products applied to generate a new product. In the NASA-funded Instant Karma project, we examine provenance capture in earth science applications, specifically the Advanced Microwave Scanning Radiometer - Earth Observing System (AMSR-E) Science Investigator-led Processing system (SIPS). The project is integrating the Karma provenance collection and representation tool into the AMSR-E SIPS production environment, with an initial focus on Sea Ice. This presentation will describe capture and representation of provenance that is guided by the Open Provenance Model (OPM). Several things have become clear during the course of the project to date. One is that core OPM entities and relationships are not adequate for expressing the kinds of provenance that is of interest in the science domain. OPM supports name-value pair annotations that can be used to augment what is known about the provenance entities and relationships, but in Karma, annotations cannot be added during capture, but only after the fact. This limits the capture system's ability to record something it learned about an entity after the event of its creation in the provenance record. We will discuss extensions to the Open Provenance Model (OPM) and modifications to the Karma tool suite to address this issue, more efficient representations of earth science kinds of provenance, and definition of metadata structures for capturing related knowledge about the data products and science algorithms used to generate them. Use scenarios for provenance information is an active topic of investigation. It has additionally become clear through the project that not all provenance is created equal. In processing pipelines, some provenance is repetitive and uninteresting. Because of the volume of provenance, this obscures what are the interesting pieces of provenance. Methodologies to reveal science-relevant provenance will be presented, along with a preview of the AMSR-E Provenance Browser.

Multi-frame knowledge based text enhancement for mobile phone captured videos

NASA Astrophysics Data System (ADS)

Ozarslan, Suleyman; Eren, P. Erhan

2014-02-01

In this study, we explore automated text recognition and enhancement using mobile phone captured videos of store receipts. We propose a method which includes Optical Character Resolution (OCR) enhanced by our proposed Row Based Multiple Frame Integration (RB-MFI), and Knowledge Based Correction (KBC) algorithms. In this method, first, the trained OCR engine is used for recognition; then, the RB-MFI algorithm is applied to the output of the OCR. The RB-MFI algorithm determines and combines the most accurate rows of the text outputs extracted by using OCR from multiple frames of the video. After RB-MFI, KBC algorithm is applied to these rows to correct erroneous characters. Results of the experiments show that the proposed video-based approach which includes the RB-MFI and the KBC algorithm increases the word character recognition rate to 95%, and the character recognition rate to 98%.

Advanced Video Activity Analytics (AVAA): Human Factors Evaluation

DTIC Science & Technology

2015-05-01

video, and 3) creating and saving annotations (Fig. 11). (The logging program was updated after the pilot to also capture search clicks.) Playing and... visual search task and the auditory task together and thus automatically focused on the visual task. Alternatively, the operator may have intentionally...affect performance on the primary task; however, in the current test there was no apparent effect on the operator’s performance in the visual search task

Automatic extraction of angiogenesis bioprocess from text

PubMed Central

Wang, Xinglong; McKendrick, Iain; Barrett, Ian; Dix, Ian; French, Tim; Tsujii, Jun'ichi; Ananiadou, Sophia

2011-01-01

Motivation: Understanding key biological processes (bioprocesses) and their relationships with constituent biological entities and pharmaceutical agents is crucial for drug design and discovery. One way to harvest such information is searching the literature. However, bioprocesses are difficult to capture because they may occur in text in a variety of textual expressions. Moreover, a bioprocess is often composed of a series of bioevents, where a bioevent denotes changes to one or a group of cells involved in the bioprocess. Such bioevents are often used to refer to bioprocesses in text, which current techniques, relying solely on specialized lexicons, struggle to find. Results: This article presents a range of methods for finding bioprocess terms and events. To facilitate the study, we built a gold standard corpus in which terms and events related to angiogenesis, a key biological process of the growth of new blood vessels, were annotated. Statistics of the annotated corpus revealed that over 36% of the text expressions that referred to angiogenesis appeared as events. The proposed methods respectively employed domain-specific vocabularies, a manually annotated corpus and unstructured domain-specific documents. Evaluation results showed that, while a supervised machine-learning model yielded the best precision, recall and F1 scores, the other methods achieved reasonable performance and less cost to develop. Availability: The angiogenesis vocabularies, gold standard corpus, annotation guidelines and software described in this article are available at http://text0.mib.man.ac.uk/~mbassxw2/angiogenesis/ Contact: xinglong.wang@gmail.com PMID:21821664

Model and Interoperability using Meta Data Annotations

NASA Astrophysics Data System (ADS)

David, O.

2011-12-01

Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside. While providing all those capabilities, a significant reduction in the size of the model source code was achieved. To support the benefit of annotations for a modeler, studies were conducted to evaluate the effectiveness of an annotation based framework approach with other modeling frameworks and libraries, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A typical hydrological model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. Experience to date has demonstrated the multi-purpose value of using annotations. Annotations are also a feasible and practical method to enable interoperability among models and modeling frameworks.

Webcams, Crowdsourcing, and Enhanced Crosswalks: Developing a Novel Method to Analyze Active Transportation.

PubMed

Hipp, J Aaron; Manteiga, Alicia; Burgess, Amanda; Stylianou, Abby; Pless, Robert

2016-01-01

Active transportation opportunities and infrastructure are an important component of a community's design, livability, and health. Features of the built environment influence active transportation, but objective study of the natural experiment effects of built environment improvements on active transportation is challenging. The purpose of this study was to develop and present a novel method of active transportation research using webcams and crowdsourcing, and to determine if crosswalk enhancement was associated with changes in active transportation rates, including across a variety of weather conditions. The 20,529 publicly available webcam images from two street intersections in Washington, DC, USA were used to examine the impact of an improved crosswalk on active transportation. A crowdsource, Amazon Mechanical Turk, annotated image data. Temperature data were collected from the National Oceanic and Atmospheric Administration, and precipitation data were annotated from images by trained research assistants. Summary analyses demonstrated slight, bi-directional differences in the percent of images with pedestrians and bicyclists captured before and after the enhancement of the crosswalks. Chi-square analyses revealed these changes were not significant. In general, pedestrian presence increased in images captured during moderate temperatures compared to images captured during hot or cold temperatures. Chi-square analyses indicated the crosswalk improvement may have encouraged walking and biking in uncomfortable outdoor conditions (P < 0.5). The methods employed provide an objective, cost-effective alternative to traditional means of examining the effects of built environment changes on active transportation. The use of webcams to collect active transportation data has applications for community policymakers, planners, and health professionals. Future research will work to validate this method in a variety of settings as well as across different built environment and community policy initiatives.

Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics.

PubMed

Percha, Bethany; Altman, Russ B

2013-01-01

The biomedical literature presents a uniquely challenging text mining problem. Sentences are long and complex, the subject matter is highly specialized with a distinct vocabulary, and producing annotated training data for this domain is time consuming and expensive. In this environment, unsupervised text mining methods that do not rely on annotated training data are valuable. Here we investigate the use of random indexing, an automated method for producing vector-space semantic representations of words from large, unlabeled corpora, to address the problem of term normalization in sentences describing drugs and genes. We show that random indexing produces similarity scores that capture some of the structure of PHARE, a manually curated ontology of pharmacogenomics concepts. We further show that random indexing can be used to identify likely word candidates for inclusion in the ontology, and can help localize these new labels among classes and roles within the ontology.

Inferring the semantic relationships of words within an ontology using random indexing: applications to pharmacogenomics

PubMed Central

Percha, Bethany; Altman, Russ B.

2013-01-01

The biomedical literature presents a uniquely challenging text mining problem. Sentences are long and complex, the subject matter is highly specialized with a distinct vocabulary, and producing annotated training data for this domain is time consuming and expensive. In this environment, unsupervised text mining methods that do not rely on annotated training data are valuable. Here we investigate the use of random indexing, an automated method for producing vector-space semantic representations of words from large, unlabeled corpora, to address the problem of term normalization in sentences describing drugs and genes. We show that random indexing produces similarity scores that capture some of the structure of PHARE, a manually curated ontology of pharmacogenomics concepts. We further show that random indexing can be used to identify likely word candidates for inclusion in the ontology, and can help localize these new labels among classes and roles within the ontology. PMID:24551397

Analysis of mammalian gene function through broad based phenotypic screens across a consortium of mouse clinics

PubMed Central

Adams, David J; Adams, Niels C; Adler, Thure; Aguilar-Pimentel, Antonio; Ali-Hadji, Dalila; Amann, Gregory; André, Philippe; Atkins, Sarah; Auburtin, Aurelie; Ayadi, Abdel; Becker, Julien; Becker, Lore; Bedu, Elodie; Bekeredjian, Raffi; Birling, Marie-Christine; Blake, Andrew; Bottomley, Joanna; Bowl, Mike; Brault, Véronique; Busch, Dirk H; Bussell, James N; Calzada-Wack, Julia; Cater, Heather; Champy, Marie-France; Charles, Philippe; Chevalier, Claire; Chiani, Francesco; Codner, Gemma F; Combe, Roy; Cox, Roger; Dalloneau, Emilie; Dierich, André; Di Fenza, Armida; Doe, Brendan; Duchon, Arnaud; Eickelberg, Oliver; Esapa, Chris T; El Fertak, Lahcen; Feigel, Tanja; Emelyanova, Irina; Estabel, Jeanne; Favor, Jack; Flenniken, Ann; Gambadoro, Alessia; Garrett, Lilian; Gates, Hilary; Gerdin, Anna-Karin; Gkoutos, George; Greenaway, Simon; Glasl, Lisa; Goetz, Patrice; Da Cruz, Isabelle Goncalves; Götz, Alexander; Graw, Jochen; Guimond, Alain; Hans, Wolfgang; Hicks, Geoff; Hölter, Sabine M; Höfler, Heinz; Hancock, John M; Hoehndorf, Robert; Hough, Tertius; Houghton, Richard; Hurt, Anja; Ivandic, Boris; Jacobs, Hughes; Jacquot, Sylvie; Jones, Nora; Karp, Natasha A; Katus, Hugo A; Kitchen, Sharon; Klein-Rodewald, Tanja; Klingenspor, Martin; Klopstock, Thomas; Lalanne, Valerie; Leblanc, Sophie; Lengger, Christoph; le Marchand, Elise; Ludwig, Tonia; Lux, Aline; McKerlie, Colin; Maier, Holger; Mandel, Jean-Louis; Marschall, Susan; Mark, Manuel; Melvin, David G; Meziane, Hamid; Micklich, Kateryna; Mittelhauser, Christophe; Monassier, Laurent; Moulaert, David; Muller, Stéphanie; Naton, Beatrix; Neff, Frauke; Nolan, Patrick M; Nutter, Lauryl MJ; Ollert, Markus; Pavlovic, Guillaume; Pellegata, Natalia S; Peter, Emilie; Petit-Demoulière, Benoit; Pickard, Amanda; Podrini, Christine; Potter, Paul; Pouilly, Laurent; Puk, Oliver; Richardson, David; Rousseau, Stephane; Quintanilla-Fend, Leticia; Quwailid, Mohamed M; Racz, Ildiko; Rathkolb, Birgit; Riet, Fabrice; Rossant, Janet; Roux, Michel; Rozman, Jan; Ryder, Ed; Salisbury, Jennifer; Santos, Luis; Schäble, Karl-Heinz; Schiller, Evelyn; Schrewe, Anja; Schulz, Holger; Steinkamp, Ralf; Simon, Michelle; Stewart, Michelle; Stöger, Claudia; Stöger, Tobias; Sun, Minxuan; Sunter, David; Teboul, Lydia; Tilly, Isabelle; Tocchini-Valentini, Glauco P; Tost, Monica; Treise, Irina; Vasseur, Laurent; Velot, Emilie; Vogt-Weisenhorn, Daniela; Wagner, Christelle; Walling, Alison; Weber, Bruno; Wendling, Olivia; Westerberg, Henrik; Willershäuser, Monja; Wolf, Eckhard; Wolter, Anne; Wood, Joe; Wurst, Wolfgang; Yildirim, Ali Önder; Zeh, Ramona; Zimmer, Andreas; Zimprich, Annemarie

2015-01-01

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse ES cell knockout resource provides a basis for characterisation of relationships between gene and phenotype. The EUMODIC consortium developed and validated robust methodologies for broad-based phenotyping of knockouts through a pipeline comprising 20 disease-orientated platforms. We developed novel statistical methods for pipeline design and data analysis aimed at detecting reproducible phenotypes with high power. We acquired phenotype data from 449 mutant alleles, representing 320 unique genes, of which half had no prior functional annotation. We captured data from over 27,000 mice finding that 83% of the mutant lines are phenodeviant, with 65% demonstrating pleiotropy. Surprisingly, we found significant differences in phenotype annotation according to zygosity. Novel phenotypes were uncovered for many genes with unknown function providing a powerful basis for hypothesis generation and further investigation in diverse systems. PMID:26214591

Supporting Handoff in Asynchronous Collaborative Sensemaking Using Knowledge-Transfer Graphs.

PubMed

Zhao, Jian; Glueck, Michael; Isenberg, Petra; Chevalier, Fanny; Khan, Azam

2018-01-01

During asynchronous collaborative analysis, handoff of partial findings is challenging because externalizations produced by analysts may not adequately communicate their investigative process. To address this challenge, we developed techniques to automatically capture and help encode tacit aspects of the investigative process based on an analyst's interactions, and streamline explicit authoring of handoff annotations. We designed our techniques to mediate awareness of analysis coverage, support explicit communication of progress and uncertainty with annotation, and implicit communication through playback of investigation histories. To evaluate our techniques, we developed an interactive visual analysis system, KTGraph, that supports an asynchronous investigative document analysis task. We conducted a two-phase user study to characterize a set of handoff strategies and to compare investigative performance with and without our techniques. The results suggest that our techniques promote the use of more effective handoff strategies, help increase an awareness of prior investigative process and insights, as well as improve final investigative outcomes.

Interpretation and mapping of geological features using mobile devices for 3D outcrop modelling

NASA Astrophysics Data System (ADS)

Buckley, Simon J.; Kehl, Christian; Mullins, James R.; Howell, John A.

2016-04-01

Advances in 3D digital geometric characterisation have resulted in widespread adoption in recent years, with photorealistic models utilised for interpretation, quantitative and qualitative analysis, as well as education, in an increasingly diverse range of geoscience applications. Topographic models created using lidar and photogrammetry, optionally combined with imagery from sensors such as hyperspectral and thermal cameras, are now becoming commonplace in geoscientific research. Mobile devices (tablets and smartphones) are maturing rapidly to become powerful field computers capable of displaying and interpreting 3D models directly in the field. With increasingly high-quality digital image capture, combined with on-board sensor pose estimation, mobile devices are, in addition, a source of primary data, which can be employed to enhance existing geological models. Adding supplementary image textures and 2D annotations to photorealistic models is therefore a desirable next step to complement conventional field geoscience. This contribution reports on research into field-based interpretation and conceptual sketching on images and photorealistic models on mobile devices, motivated by the desire to utilise digital outcrop models to generate high quality training images (TIs) for multipoint statistics (MPS) property modelling. Representative training images define sedimentological concepts and spatial relationships between elements in the system, which are subsequently modelled using artificial learning to populate geocellular models. Photorealistic outcrop models are underused sources of quantitative and qualitative information for generating TIs, explored further in this research by linking field and office workflows through the mobile device. Existing textured models are loaded to the mobile device, allowing rendering in a 3D environment. Because interpretation in 2D is more familiar and comfortable for users, the developed application allows new images to be captured with the device's digital camera, and an interface is available for annotating (interpreting) the image using lines and polygons. Image-to-geometry registration is then performed using a developed algorithm, initialised using the coarse pose from the on-board orientation and positioning sensors. The annotations made on the captured images are then available in the 3D model coordinate system for overlay and export. This workflow allows geologists to make interpretations and conceptual models in the field, which can then be linked to and refined in office workflows for later MPS property modelling.

HapMap tagSNP transferability in multiple populations: general guidelines

PubMed Central

Xing, Jinchuan; Witherspoon, David J.; Watkins, W. Scott; Zhang, Yuhua; Tolpinrud, Whitney; Jorde, Lynn B.

2008-01-01

This PDF receipt will only be used as the basis for generating PubMed Central (PMC) documents. PMC documents will be made available for review after conversion (approx. 2–3 weeks time). Any corrections that need to be made will be done at that time. No materials will be released to PMC without the approval of an author. Only the PMC documents will appear on PubMed Central -- this PDF Receipt will not appear on PubMed Central. Linkage disequilibrium (LD) has received much recent attention because of its value in localizing disease-causing genes. Due to the extensive LD between neighboring loci in the human genome, it is believed that a subset of the single nucleotide polymorphisms in a region (tagSNPs) can be selected to capture most of the remaining SNP variants. In this study, we examined LD patterns and HapMap tagSNP transferability in more than 300 individuals. A South Indian and an African Mbuti Pygmy population sample were included to evaluate the performance of HapMap tagSNPs in geographically distinct and genetically isolated populations. Our results show that HapMap tagSNPs selected with r2 >= 0.8 can capture more than 85% of the SNPs in populations that are from the same continental group. Combined tagSNPs from HapMap CEU and CHB+JPT serve as the best reference for the Indian sample. The HapMap YRI are a sufficient reference for tagSNP selection in the Pygmy sample. In addition to our findings, we reviewed over 25 recent studies of tagSNP transferability and propose a general guideline for selecting tagSNPs from HapMap populations. PMID:18482828

Identifying and Overcoming Obstacles to Point-of-Care Data Collection for Eye Care Professionals

PubMed Central

Lobach, David F.; Silvey, Garry M.; Macri, Jennifer M.; Hunt, Megan; Kacmaz, Roje O.; Lee, Paul P.

2005-01-01

Supporting data entry by clinicians is considered one of the greatest challenges in implementing electronic health records. In this paper we describe a formative evaluation study using three different methodologies through which we identified obstacles to point-of-care data entry for eye care and then used the formative process to develop and test solutions to overcome these obstacles. The greatest obstacles were supporting free text annotation of clinical observations and accommodating the creation of detailed diagrams in multiple colors. To support free text entry, we arrived at an approach that captures an image of a free text note and associates this image with related data elements in an encounter note. The detailed diagrams included a color pallet that allowed changing pen color with a single stroke and also captured the diagrams as an image associated with related data elements. During observed sessions with simulated patients, these approaches satisfied the clinicians’ documentation needs by capturing the full range of clinical complexity that arises in practice. PMID:16779083

The GENCODE exome: sequencing the complete human exome

PubMed Central

Coffey, Alison J; Kokocinski, Felix; Calafato, Maria S; Scott, Carol E; Palta, Priit; Drury, Eleanor; Joyce, Christopher J; LeProust, Emily M; Harrow, Jen; Hunt, Sarah; Lehesjoki, Anna-Elina; Turner, Daniel J; Hubbard, Tim J; Palotie, Aarno

2011-01-01

Sequencing the coding regions, the exome, of the human genome is one of the major current strategies to identify low frequency and rare variants associated with human disease traits. So far, the most widely used commercial exome capture reagents have mainly targeted the consensus coding sequence (CCDS) database. We report the design of an extended set of targets for capturing the complete human exome, based on annotation from the GENCODE consortium. The extended set covers an additional 5594 genes and 10.3 Mb compared with the current CCDS-based sets. The additional regions include potential disease genes previously inaccessible to exome resequencing studies, such as 43 genes linked to ion channel activity and 70 genes linked to protein kinase activity. In total, the new GENCODE exome set developed here covers 47.9 Mb and performed well in sequence capture experiments. In the sample set used in this study, we identified over 5000 SNP variants more in the GENCODE exome target (24%) than in the CCDS-based exome sequencing. PMID:21364695

Online coupled camera pose estimation and dense reconstruction from video

DOEpatents

Medioni, Gerard; Kang, Zhuoliang

2016-11-01

A product may receive each image in a stream of video image of a scene, and before processing the next image, generate information indicative of the position and orientation of an image capture device that captured the image at the time of capturing the image. The product may do so by identifying distinguishable image feature points in the image; determining a coordinate for each identified image feature point; and for each identified image feature point, attempting to identify one or more distinguishable model feature points in a three dimensional (3D) model of at least a portion of the scene that appears likely to correspond to the identified image feature point. Thereafter, the product may find each of the following that, in combination, produce a consistent projection transformation of the 3D model onto the image: a subset of the identified image feature points for which one or more corresponding model feature points were identified; and, for each image feature point that has multiple likely corresponding model feature points, one of the corresponding model feature points. The product may update a 3D model of at least a portion of the scene following the receipt of each video image and before processing the next video image base on the generated information indicative of the position and orientation of the image capture device at the time of capturing the received image. The product may display the updated 3D model after each update to the model.

MiMiR – an integrated platform for microarray data sharing, mining and analysis

PubMed Central

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-01-01

Background Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. Results A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. Conclusion The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies. PMID:18801157

MiMiR--an integrated platform for microarray data sharing, mining and analysis.

PubMed

Tomlinson, Chris; Thimma, Manjula; Alexandrakis, Stelios; Castillo, Tito; Dennis, Jayne L; Brooks, Anthony; Bradley, Thomas; Turnbull, Carly; Blaveri, Ekaterini; Barton, Geraint; Chiba, Norie; Maratou, Klio; Soutter, Pat; Aitman, Tim; Game, Laurence

2008-09-18

Despite considerable efforts within the microarray community for standardising data format, content and description, microarray technologies present major challenges in managing, sharing, analysing and re-using the large amount of data generated locally or internationally. Additionally, it is recognised that inconsistent and low quality experimental annotation in public data repositories significantly compromises the re-use of microarray data for meta-analysis. MiMiR, the Microarray data Mining Resource was designed to tackle some of these limitations and challenges. Here we present new software components and enhancements to the original infrastructure that increase accessibility, utility and opportunities for large scale mining of experimental and clinical data. A user friendly Online Annotation Tool allows researchers to submit detailed experimental information via the web at the time of data generation rather than at the time of publication. This ensures the easy access and high accuracy of meta-data collected. Experiments are programmatically built in the MiMiR database from the submitted information and details are systematically curated and further annotated by a team of trained annotators using a new Curation and Annotation Tool. Clinical information can be annotated and coded with a clinical Data Mapping Tool within an appropriate ethical framework. Users can visualise experimental annotation, assess data quality, download and share data via a web-based experiment browser called MiMiR Online. All requests to access data in MiMiR are routed through a sophisticated middleware security layer thereby allowing secure data access and sharing amongst MiMiR registered users prior to publication. Data in MiMiR can be mined and analysed using the integrated EMAAS open source analysis web portal or via export of data and meta-data into Rosetta Resolver data analysis package. The new MiMiR suite of software enables systematic and effective capture of extensive experimental and clinical information with the highest MIAME score, and secure data sharing prior to publication. MiMiR currently contains more than 150 experiments corresponding to over 3000 hybridisations and supports the Microarray Centre's large microarray user community and two international consortia. The MiMiR flexible and scalable hardware and software architecture enables secure warehousing of thousands of datasets, including clinical studies, from microarray and potentially other -omics technologies.

Representing virus-host interactions and other multi-organism processes in the Gene Ontology.

PubMed

Foulger, R E; Osumi-Sutherland, D; McIntosh, B K; Hulo, C; Masson, P; Poux, S; Le Mercier, P; Lomax, J

2015-07-28

The Gene Ontology project is a collaborative effort to provide descriptions of gene products in a consistent and computable language, and in a species-independent manner. The Gene Ontology is designed to be applicable to all organisms but up to now has been largely under-utilized for prokaryotes and viruses, in part because of a lack of appropriate ontology terms. To address this issue, we have developed a set of Gene Ontology classes that are applicable to microbes and their hosts, improving both coverage and quality in this area of the Gene Ontology. Describing microbial and viral gene products brings with it the additional challenge of capturing both the host and the microbe. Recognising this, we have worked closely with annotation groups to test and optimize the GO classes, and we describe here a set of annotation guidelines that allow the controlled description of two interacting organisms. Building on the microbial resources already in existence such as ViralZone, UniProtKB keywords and MeGO, this project provides an integrated ontology to describe interactions between microbial species and their hosts, with mappings to the external resources above. Housing this information within the freely-accessible Gene Ontology project allows the classes and annotation structure to be utilized by a large community of biologists and users.

The Disease Portals, disease-gene annotation and the RGD disease ontology at the Rat Genome Database.

PubMed

Hayman, G Thomas; Laulederkind, Stanley J F; Smith, Jennifer R; Wang, Shur-Jen; Petri, Victoria; Nigam, Rajni; Tutaj, Marek; De Pons, Jeff; Dwinell, Melinda R; Shimoyama, Mary

2016-01-01

The Rat Genome Database (RGD;http://rgd.mcw.edu/) provides critical datasets and software tools to a diverse community of rat and non-rat researchers worldwide. To meet the needs of the many users whose research is disease oriented, RGD has created a series of Disease Portals and has prioritized its curation efforts on the datasets important to understanding the mechanisms of various diseases. Gene-disease relationships for three species, rat, human and mouse, are annotated to capture biomarkers, genetic associations, molecular mechanisms and therapeutic targets. To generate gene-disease annotations more effectively and in greater detail, RGD initially adopted the MEDIC disease vocabulary from the Comparative Toxicogenomics Database and adapted it for use by expanding this framework with the addition of over 1000 terms to create the RGD Disease Ontology (RDO). The RDO provides the foundation for, at present, 10 comprehensive disease area-related dataset and analysis platforms at RGD, the Disease Portals. Two major disease areas are the focus of data acquisition and curation efforts each year, leading to the release of the related Disease Portals. Collaborative efforts to realize a more robust disease ontology are underway. Database URL:http://rgd.mcw.edu. © The Author(s) 2016. Published by Oxford University Press.

Curation of food-relevant chemicals in ToxCast.

PubMed

Karmaus, Agnes L; Trautman, Thomas D; Krishan, Mansi; Filer, Dayne L; Fix, Laurel A

2017-05-01

High-throughput in vitro assays and exposure prediction efforts are paving the way for modeling chemical risk; however, the utility of such extensive datasets can be limited or misleading when annotation fails to capture current chemical usage. To address this data gap and provide context for food-use in the United States (US), manual curation of food-relevant chemicals in ToxCast was conducted. Chemicals were categorized into three food-use categories: (1) direct food additives, (2) indirect food additives, or (3) pesticide residues. Manual curation resulted in 30% of chemicals having new annotation as well as the removal of 319 chemicals, most due to cancellation or only foreign usage. These results highlight that manual curation of chemical use information provided significant insight affecting the overall inventory and chemical categorization. In total, 1211 chemicals were confirmed as current day food-use in the US by manual curation; 1154 of these chemicals were also identified as food-related in the globally sourced chemical use information from Chemical/Product Categories database (CPCat). The refined list of food-use chemicals and the sources highlighted for compiling annotated information required to confirm food-use are valuable resources for providing needed context when evaluating large-scale inventories such as ToxCast. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Semantic attributes for people's appearance description: an appearance modality for video surveillance applications

NASA Astrophysics Data System (ADS)

Frikha, Mayssa; Fendri, Emna; Hammami, Mohamed

2017-09-01

Using semantic attributes such as gender, clothes, and accessories to describe people's appearance is an appealing modeling method for video surveillance applications. We proposed a midlevel appearance signature based on extracting a list of nameable semantic attributes describing the body in uncontrolled acquisition conditions. Conventional approaches extract the same set of low-level features to learn the semantic classifiers uniformly. Their critical limitation is the inability to capture the dominant visual characteristics for each trait separately. The proposed approach consists of extracting low-level features in an attribute-adaptive way by automatically selecting the most relevant features for each attribute separately. Furthermore, relying on a small training-dataset would easily lead to poor performance due to the large intraclass and interclass variations. We annotated large scale people images collected from different person reidentification benchmarks covering a large attribute sample and reflecting the challenges of uncontrolled acquisition conditions. These annotations were gathered into an appearance semantic attribute dataset that contains 3590 images annotated with 14 attributes. Various experiments prove that carefully designed features for learning the visual characteristics for an attribute provide an improvement of the correct classification accuracy and a reduction of both spatial and temporal complexities against state-of-the-art approaches.

Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification.

PubMed

de Miguel, Marina; Cabezas, José-Antonio; de María, Nuria; Sánchez-Gómez, David; Guevara, María-Ángeles; Vélez, María-Dolores; Sáez-Laguna, Enrique; Díaz, Luis-Manuel; Mancha, Jose-Antonio; Barbero, María-Carmen; Collada, Carmen; Díaz-Sala, Carmen; Aranda, Ismael; Cervera, María-Teresa

2014-06-12

Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in a Mediterranean conifer and tested their stability under drought. High density linkage maps for Pinus pinaster were used in the detection of QTL for photosynthesis and water use efficiency at three water irrigation regimes. A total of 28 significant and 27 suggestive QTL were found. QTL detected for photochemical traits accounted for the higher percentage of phenotypic variance. Functional annotation of genes within the QTL suggested 58 candidate genes for the analyzed traits. Allele association analysis in selected candidate genes showed three SNPs located in a MYB transcription factor that were significantly associated with efficiency of energy capture by open PSII reaction centers and specific leaf area. The integration of QTL mapping of functional traits, genome annotation and allele association yielded several candidate genes involved with molecular control of photosynthesis and water use efficiency in response to drought in a conifer species. The results obtained highlight the importance of maintaining the integrity of the photochemical machinery in P. pinaster drought response.

Multi-Omics Driven Assembly and Annotation of the Sandalwood (Santalum album) Genome.

PubMed

Mahesh, Hirehally Basavarajegowda; Subba, Pratigya; Advani, Jayshree; Shirke, Meghana Deepak; Loganathan, Ramya Malarini; Chandana, Shankara Lingu; Shilpa, Siddappa; Chatterjee, Oishi; Pinto, Sneha Maria; Prasad, Thottethodi Subrahmanya Keshava; Gowda, Malali

2018-04-01

Indian sandalwood ( Santalum album ) is an important tropical evergreen tree known for its fragrant heartwood-derived essential oil and its valuable carving wood. Here, we applied an integrated genomic, transcriptomic, and proteomic approach to assemble and annotate the Indian sandalwood genome. Our genome sequencing resulted in the establishment of a draft map of the smallest genome for any woody tree species to date (221 Mb). The genome annotation predicted 38,119 protein-coding genes and 27.42% repetitive DNA elements. In-depth proteome analysis revealed the identities of 72,325 unique peptides, which confirmed 10,076 of the predicted genes. The addition of transcriptomic and proteogenomic approaches resulted in the identification of 53 novel proteins and 34 gene-correction events that were missed by genomic approaches. Proteogenomic analysis also helped in reassigning 1,348 potential noncoding RNAs as bona fide protein-coding messenger RNAs. Gene expression patterns at the RNA and protein levels indicated that peptide sequencing was useful in capturing proteins encoded by nuclear and organellar genomes alike. Mass spectrometry-based proteomic evidence provided an unbiased approach toward the identification of proteins encoded by organellar genomes. Such proteins are often missed in transcriptome data sets due to the enrichment of only messenger RNAs that contain poly(A) tails. Overall, the use of integrated omic approaches enhanced the quality of the assembly and annotation of this nonmodel plant genome. The availability of genomic, transcriptomic, and proteomic data will enhance genomics-assisted breeding, germplasm characterization, and conservation of sandalwood trees. © 2018 American Society of Plant Biologists. All Rights Reserved.

Long-read sequencing of the coffee bean transcriptome reveals the diversity of full-length transcripts

PubMed Central

Cheng, Bing; Furtado, Agnelo

2017-01-01

Abstract Polyploidization contributes to the complexity of gene expression, resulting in numerous related but different transcripts. This study explored the transcriptome diversity and complexity of the tetraploid Arabica coffee (Coffea arabica) bean. Long-read sequencing (LRS) by Pacbio Isoform sequencing (Iso-seq) was used to obtain full-length transcripts without the difficulty and uncertainty of assembly required for reads from short-read technologies. The tetraploid transcriptome was annotated and compared with data from the sub-genome progenitors. Caffeine and sucrose genes were targeted for case analysis. An isoform-level tetraploid coffee bean reference transcriptome with 95 995 distinct transcripts (average 3236 bp) was obtained. A total of 88 715 sequences (92.42%) were annotated with BLASTx against NCBI non-redundant plant proteins, including 34 719 high-quality annotations. Further BLASTn analysis against NCBI non-redundant nucleotide sequences, Coffea canephora coding sequences with UTR, C. arabica ESTs, and Rfam resulted in 1213 sequences without hits, were potential novel genes in coffee. Longer UTRs were captured, especially in the 5΄UTRs, facilitating the identification of upstream open reading frames. The LRS also revealed more and longer transcript variants in key caffeine and sucrose metabolism genes from this polyploid genome. Long sequences (>10 kilo base) were poorly annotated. LRS technology shows the limitation of previous studies. It provides an important tool to produce a reference transcriptome including more of the diversity of full-length transcripts to help understand the biology and support the genetic improvement of polyploid species such as coffee. PMID:29048540

When a Home is Not a Home: MultiDrug-Resistant Organism (MDRO) Colonization and Environmental Contamination in 28 Nursing Homes (NHs)

PubMed Central

McKinnell, James A; Miller, Loren; Singh, Raveena D; Mendez, Job; Franco, Ryan; Gussin, Gabrielle; Chang, Justin; Dutciuc, Tabitha D; Saavedra, Raheeb; Kleinman, Ken; Peterson, Ellena M; Evans, Kaye D; Heim, Lauren; Miner, Aaron; Estevez, Marlene; Custodio, Harold; Yamaguchi, Stacey; Nguyen, Jenny; Varasteh, Alex; Launer, Bryn; Agrawal, Shalini; Tjoa, Thomas; He, Jiayi; Park, Steven; Tam, Steven; Gohil, Shruti K; Stone, Nimalie D; Steinberg, Karl; Montgomery, Jocelyn; Beecham, Nancy; Huang, Susan S

2017-01-01

Abstract Background The majority of healthcare-associated infections due to MDROs occur in the post-discharge setting. Understanding MDRO spread and containment in NHs can help identify infection prevention activities needed to care for vulnerable patients in a medical home setting. Methods We conducted a baseline point prevalence study of MDRO colonization in residents of 28 Southern California NHs participating in a decolonization trial. In Fall 2016, residents were randomly sampled to obtain a set of 50 nares and skin (axilla/groin) swabs from each NH. Nasal swabs were processed for MRSA and skin swabs were processed for MRSA, VRE, ESBL, and CRE. In addition, environmental swabs were collected from high touch objects in resident rooms (bedrail, call button/TV remote, door knobs, light switch, bathroom) and common areas (nursing station, table, chair, railing, and drinking fountain). Results A total of 2,797 body swabs were obtained from 1400 residents. Overall, 48.6% (N = 680) of residents harbored MDROs. MRSA was found in 37% of residents (29.5% nares, 24.4% skin), followed by ESBL in 16% (Table 1). Resident MDRO status was only known for 11% of MRSA (59/518), 18% ESBL (40/228), 4% VRE (4/99), and none of the CRE (0/13) carriers. Colonization did not differ between long stay (48.8%, 534/1094) vs. post-acute (47.7%, 146/306) residents (P = NS), but bedbound residents were more likely to be MDRO colonized (58.7%, 182/310) vs. ambulatory residents (45.7%, 497/1088, P < 0.001). A total of 560 environmental swabs were obtained with 93% of common areas and 74% of resident rooms having an MDRO+ object with an average of 2.5 and 1.9 objects found to be contaminated (Table 2). Conclusion One in two NH residents are colonized with MDROs, which is largely unknown to the facility. MDRO carriage is associated with total care needs, but not long stay status. Environmental contamination in resident rooms and common areas is common. The burden of MDRO colonization and contamination is sufficiently high that universal strategies to reduce colonization and transmission are warranted. Disclosures J. A. McKinnell, Allergan: Research Contractor, Scientific Advisor and Speaker’s Bureau, Consulting fee, Research support and Speaker honorarium; Achaogen: Research Contractor, Scientific Advisor and Shareholder, Research support; Cempra: Research Contractor and Scientific Advisor, Research support; Theravance: Research Contractor, Research support; Science 37: Research Contractor, Salary; Expert Stewardship, LLC: Board Member and Employee, Salary; Thermo Fisher: Scientific Advisor, Salary; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; L. Miller, 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; R. D. Singh, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; J. Mendez, Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; R. Franco, Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; G. Gussin, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; L’Oreal: Consultant, Consulting fee; J. Chang, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; T. D. Dutciuc, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; R. Saavedra, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; K. Kleinman, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Molnlycke: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; E. M. Peterson, Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; L. Heim, Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; A. Miner, Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; M. Estevez, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; H. Custodio, Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. Yamaguchi, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; J. Nguyen, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; A. Varasteh, Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Product: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; B. Launer, 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. Agrawal, Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; T. Tjoa, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; J. He, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. Park, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. Tam, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. K. Gohil, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. S. Huang, Sage Products: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product; Clorox: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product; 3M: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product; Molnlycke: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product

Identification of Technology Terms in Patents (Open Access, Published Version)

DTIC Science & Technology

2014-05-31

large set of human anno - tated examples of the target class(es) along with their tex- tual contexts to serve as training examples for generating a machine...perform the equiva- lent function in German and Chinese. 2.2. Manual annotation of terms Supervised learning requires a gold set of manually anno ...Npr, prev Jpr, prev J ). These were intended to capture, for ex- ample, the verb (and any prepositions/articles) for which the term is the object. prev

The Human Variome Project (HVP) 2009 Forum "Towards Establishing Standards".

PubMed

Howard, Heather J; Horaitis, Ourania; Cotton, Richard G H; Vihinen, Mauno; Dalgleish, Raymond; Robinson, Peter; Brookes, Anthony J; Axton, Myles; Hoffmann, Robert; Tuffery-Giraud, Sylvie

2010-03-01

The May 2009 Human Variome Project (HVP) Forum "Towards Establishing Standards" was a round table discussion attended by delegates from groups representing international efforts aimed at standardizing several aspects of the HVP: mutation nomenclature, description and annotation, clinical ontology, means to better characterize unclassified variants (UVs), and methods to capture mutations from diagnostic laboratories for broader distribution to the medical genetics research community. Methods for researchers to receive credit for their effort at mutation detection were also discussed. (c) 2010 Wiley-Liss, Inc.

The CDC SHIELD Orange County Project – Baseline Multi Drug-Resistant Organism (MDRO) Prevalence in a Southern California Region

PubMed Central

Singh, Raveena D; Jernigan, John A; Slayton, Rachel B; Stone, Nimalie D; McKinnell, James A; Miller, Loren G; Kleinman, Ken; Heim, Lauren; Dutciuc, Tabitha D; Estevez, Marlene; Gussin, Gabrielle; Chang, Justin; Peterson, Ellena M; Evans, Kaye D; Lee, Bruce Y; Mueller, Leslie E; Bartsch, Sarah M; Zahn, Matthew; Janssen, Lynn; Weinstein, Robert A; Hayden, Mary K; Gohil, Shruti K; Park, Steven; Tam, Steven; Saavedra, Raheeb; Yamaguchi, Stacey; Custodio, Harold; Nguyen, Jenny; Tjoa, Thomas; He, Jiayi; O’Donnell, Kathleen; Coady, Micaela H; Platt, Richard; Huang, Susan S

2017-01-01

Abstract Background MDROs can spread between hospitals, nursing homes (NH), and long-term acute care facilities (LTACs) via shared patients. SHIELD OC is a regional decolonization collaborative involving 38 of 104 countywide adult facilities identified by their high degree of direct and indirect patient sharing with one another. We report baseline MDRO prevalence in these facilities. Methods Adult patients in 38 facilities (17 hospitals, 18 NHs, 3 LTACs) underwent point-prevalence screening between September 2016–April 2017 for MRSA, VRE, ESBL, and CRE using nares, skin (axilla/groin), and peri-rectal swabs. In NHs and LTACs, residents were randomly selected until 50 sets of swabs were obtained. Swabbing in hospitals involved all patients in contact precautions. An additional set of swabs were also performed for all LTAC admissions from November 2016–February 2017. Results The overall prevalence of any MDRO among patients was 64% (44%–88%) in NHs, 80% (range 72%–86%) in LTACs, and 64% (54–84%) in hospitals (contact precaution patients) (Table 1). Only 25%, 64%, and 81% of patients were already known to harbor an MDRO in NHs, LTACs, and hospitals, respectively. Known MDRO patients also harbored another MDRO 49%, 63%, and 34% of the time for NHs, LTACs, and hospitals, respectively. In LTACs, MDRO point prevalence was 38% higher than the usual admission prevalence (65% higher for MRSA, 34% higher for VRE, 95% higher for ESBL, and 50% higher for CRE). Conclusion MDRO carriage in highly inter-connected NHs and LTACs was widespread, rivaling that found in hospitalized patients on contact precautions. MRSA, VRE, and ESBL carriage far outnumbered CRE carriage. A history of MDRO was insensitive for identifying MDRO carriers, and many patients carried multiple MDROs. The extensive MDRO burden and transmission in long-term care settings suggests that regional MDRO prevention efforts must include MDRO control in long-term care facilities. Disclosures R. D. Singh, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; J. A. McKinnell, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; L. G. Miller, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; K. Kleinman, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Molnlycke: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; L. Heim, Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; T. D. Dutciuc, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; M. Estevez, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; G. Gussin, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; L’Oreal: Consultant, Consulting fee; J. Chang, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; E. M. Peterson, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; B. Y. Lee, GSK: Consultant, Consulting fee; R. A. Weinstein, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Molnlycke: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; OpGen Company: Study support, Provided services at no charge; M. K. Hayden, Sage Products: Receipt of contributed product, Sage is contributing product to healthcare facilities participating in a regional collaborative on which I am a co-investigator. Neither I nor my hospital receive product.; Clorox: Receipt of contributed product, Research support; CDC: Grant Investigator and Receipt of contributed product, Research grant; Molnlycke: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; OpGen Company: Study support, Provided services at no charge for studies; S. K. Gohil, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. Park, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. Tam, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; R. Saavedra, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. Yamaguchi, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; H. Custodio, Xttrium Laboratories: Study coordination, Conducting studies in healthcare facilities that are receiving contributed product; Sage Products: Study coordination, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Study coordination, Conducting studies in healthcare facilities that are receiving contributed product; J. Nguyen, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; T. Tjoa, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; J. He, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; 3M: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; M. H. Coady, Sage Products: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Molnlycke: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; Clorox: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; R. Platt, Sage Products: Receipt of contributed product, Conducting clinical studies in which participating healthcare facilities are receiving contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting clinical studies in which participating healthcare facilities are receiving contributed product; Clorox: Receipt of contributed product, Conducting clinical studies in which participating healthcare facilities are receiving contributed product; receive research funds from Clorox, but Clorox has no role in the design; Molnlycke: Receipt of contributed product, Conducting studies in healthcare facilities that are receiving contributed product; S. S. Huang, Sage Products: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product; Xttrium Laboratories: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product; Clorox: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product; 3M: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product; Molnlycke: Receipt of contributed product, Conducting studies in which participating healthcare facilities are receiving contributed product (no contribution in submitted abstract), Participating healthcare facilities in my studies received contributed product

A computational approach to candidate gene prioritization for X-linked mental retardation using annotation-based binary filtering and motif-based linear discriminatory analysis

PubMed Central

2011-01-01

Background Several computational candidate gene selection and prioritization methods have recently been developed. These in silico selection and prioritization techniques are usually based on two central approaches - the examination of similarities to known disease genes and/or the evaluation of functional annotation of genes. Each of these approaches has its own caveats. Here we employ a previously described method of candidate gene prioritization based mainly on gene annotation, in accompaniment with a technique based on the evaluation of pertinent sequence motifs or signatures, in an attempt to refine the gene prioritization approach. We apply this approach to X-linked mental retardation (XLMR), a group of heterogeneous disorders for which some of the underlying genetics is known. Results The gene annotation-based binary filtering method yielded a ranked list of putative XLMR candidate genes with good plausibility of being associated with the development of mental retardation. In parallel, a motif finding approach based on linear discriminatory analysis (LDA) was employed to identify short sequence patterns that may discriminate XLMR from non-XLMR genes. High rates (>80%) of correct classification was achieved, suggesting that the identification of these motifs effectively captures genomic signals associated with XLMR vs. non-XLMR genes. The computational tools developed for the motif-based LDA is integrated into the freely available genomic analysis portal Galaxy (http://main.g2.bx.psu.edu/). Nine genes (APLN, ZC4H2, MAGED4, MAGED4B, RAP2C, FAM156A, FAM156B, TBL1X, and UXT) were highlighted as highly-ranked XLMR methods. Conclusions The combination of gene annotation information and sequence motif-orientated computational candidate gene prediction methods highlight an added benefit in generating a list of plausible candidate genes, as has been demonstrated for XLMR. Reviewers: This article was reviewed by Dr Barbara Bardoni (nominated by Prof Juergen Brosius); Prof Neil Smalheiser and Dr Dustin Holloway (nominated by Prof Charles DeLisi). PMID:21668950

41 CFR 301-11.25 - Must I provide receipts to substantiate my claimed travel expenses?

Code of Federal Regulations, 2014 CFR

2014-07-01

... necessary receipt(s) (see § 301-52.4 of this chapter). Note to 301-11.25: Hard copy receipts should be... chapter). You may submit a hard copy receipt, in accordance with your agency's policies, to support a...

41 CFR 301-11.25 - Must I provide receipts to substantiate my claimed travel expenses?

Code of Federal Regulations, 2012 CFR

2012-07-01

... necessary receipt(s) (see § 301-52.4 of this chapter). Note to 301-11.25: Hard copy receipts should be... chapter). You may submit a hard copy receipt, in accordance with your agency's policies, to support a...

41 CFR 301-11.25 - Must I provide receipts to substantiate my claimed travel expenses?

Code of Federal Regulations, 2013 CFR

2013-07-01

... necessary receipt(s) (see § 301-52.4 of this chapter). Note to 301-11.25: Hard copy receipts should be... chapter). You may submit a hard copy receipt, in accordance with your agency's policies, to support a...

41 CFR 301-11.25 - Must I provide receipts to substantiate my claimed travel expenses?

Code of Federal Regulations, 2011 CFR

2011-07-01

... necessary receipt(s) (see § 301-52.4 of this chapter). Note to 301-11.25: Hard copy receipts should be... chapter). You may submit a hard copy receipt, in accordance with your agency's policies, to support a...

41 CFR 301-11.25 - Must I provide receipts to substantiate my claimed travel expenses?

Code of Federal Regulations, 2010 CFR

2010-07-01

... necessary receipt(s) (see § 301-52.4 of this chapter). Note to 301-11.25: Hard copy receipts should be... chapter). You may submit a hard copy receipt, in accordance with your agency's policies, to support a...

Optical sedimentation recorder

DOEpatents

Bishop, James K.B.

2014-05-06

A robotic optical sedimentation recorder is described for the recordation of carbon flux in the oceans wherein both POC and PIC particles are captured at the open end of a submersible sampling platform, the captured particles allowed to drift down onto a collection plate where they can be imaged over time. The particles are imaged using three separate light sources, activated in sequence, one source being a back light, a second source being a side light to provide dark field illumination, and a third source comprising a cross polarized light source to illuminate birefringent particles. The recorder in one embodiment is attached to a buoyancy unit which is capable upon command for bringing the sedimentation recorder to a programmed depth below the ocean surface during recordation mode, and on command returning the unit to the ocean surface for transmission of recorded data and receipt of new instructions. The combined unit is provided with its own power source and is designed to operate autonomously in the ocean for extended periods of time.

A multi-site feasibility study for personalized medicine in canines with Osteosarcoma

PubMed Central

2013-01-01

Background A successful therapeutic strategy, specifically tailored to the molecular constitution of an individual and their disease, is an ambitious objective of modern medicine. In this report, we highlight a feasibility study in canine osteosarcoma focused on refining the infrastructure and processes required for prospective clinical trials using a series of gene expression-based Personalized Medicine (PMed) algorithms to predict suitable therapies within 5 days of sample receipt. Methods Tumor tissue samples were collected immediately following limb amputation and shipped overnight from veterinary practices. Upon receipt (day 1), RNA was extracted from snap-frozen tissue, with an adjacent H&E section for pathological diagnosis. Samples passing RNA and pathology QC were shipped to a CLIA-certified laboratory for genomic profiling. After mapping of canine probe sets to human genes and normalization against a (normal) reference set, gene level Z-scores were submitted to the PMed algorithms. The resulting PMed report was immediately forwarded to the veterinarians. Upon receipt and review of the PMed report, feedback from the practicing veterinarians was captured. Results 20 subjects were enrolled over a 5 month period. Tissue from 13 subjects passed both histological and RNA QC and were submitted for genomic analysis and subsequent PMed analysis and report generation. 11 of the 13 samples for which PMed reports were produced were communicated to the veterinarian within the target 5 business days. Of the 7 samples that failed QC, 4 were due to poor RNA quality, whereas 2 were failed following pathological review. Comments from the practicing veterinarians were generally positive and constructive, highlighting a number of areas for improvement, including enhanced education regarding PMed report interpretation, drug availability, affordable pricing and suitable canine dosing. Conclusions This feasibility trial demonstrated that with the appropriate infrastructure and processes it is possible to perform an in-depth molecular analysis of a patient’s tumor in support of real time therapeutic decision making within 5 days of sample receipt. A number of areas for improvement have been identified that should reduce the level of sample attrition and support clinical decision making. PMID:23815880

Comparing a medical records-based and a claims-based index for measuring comorbidity in patients with lung or colon cancer.

PubMed

Kehl, Kenneth L; Lamont, Elizabeth B; McNeil, Barbara J; Bozeman, Samuel R; Kelley, Michael J; Keating, Nancy L

2015-05-01

Ascertaining comorbid conditions in cancer patients is important for research and clinical quality measurement, and is particularly important for understanding care and outcomes for older patients and those with multi-morbidity. We compared the medical records-based ACE-27 index and the claims-based Charlson index in predicting receipt of therapy and survival for lung and colon cancer patients. We calculated the Charlson index using administrative data and the ACE-27 score using medical records for Veterans Affairs patients diagnosed with stage I/II non-small cell lung or stage III colon cancer from January 2003 to December 2004. We compared the proportion of patients identified by each index as having any comorbidity. We used multivariable logistic regression to ascertain the predictive power of each index regarding delivery of guideline-recommended therapies and two-year survival, comparing the c-statistic and the Akaike information criterion (AIC). Overall, 97.2% of lung and 90.9% of colon cancer patients had any comorbidity according to the ACE-27 index, versus 59.5% and 49.7%, respectively, according to the Charlson. Multivariable models including the ACE-27 index outperformed Charlson-based models when assessing receipt of guideline-recommended therapies, with higher c-statistics and lower AICs. Neither index was clearly superior in prediction of two-year survival. The ACE-27 index measured using medical records captured more comorbidity and outperformed the Charlson index measured using administrative data for predicting receipt of guideline-recommended therapies, demonstrating the potential value of more detailed comorbidity data. However, the two indices had relatively similar performance when predicting survival. Copyright © 2015 Elsevier Inc. All rights reserved.

The impact of a conditional cash transfer program on the utilization of non-targeted services: Evidence from Afghanistan.

PubMed

Witvorapong, Nopphol; Foshanji, Abo Ismael

2016-03-01

While existing research suggests that health-related conditional cash transfer (CCT) programs have positive impacts on the utilization of CCT-targeted health services, little is known as to whether they also influence the utilization of non-targeted health services-defined as general health services for which program participants are not financially motivated. Based on a sample of 6649 households in a CCT program that took place in May 2009-June 2011 in Afghanistan, we evaluate the impact of the receipt of CCTs on the utilization of non-targeted health services both by women, who were direct beneficiaries of the program, and by members of their households. We estimate the outcomes of interest through four probit models, accounting for potential endogeneity of the CCT receipt and dealing with lack of credible exclusion restrictions in different ways. In comparison with the control group, the receipt of CCTs is found to be associated with an increase in the probability of utilizing non-targeted services among household members across regression models. The results are mixed, with regard to the utilization by women, suggesting that there exist non-economic barriers to health care, unique to women, that are not captured by the data. The results confirm the importance of accounting for direct as well as indirect effects in policy evaluation and suggest that future studies investigate more deeply the role of community health workers in removing non-economic barriers for Afghan women and the possibility of introducing an incentive structure to motivate them to contribute more actively to population health in Afghanistan. Copyright © 2016 Elsevier Ltd. All rights reserved.

Expectant management of veterans with early-stage prostate cancer.

PubMed

Filson, Christopher P; Shelton, Jeremy B; Tan, Hung-Jui; Kwan, Lorna; Skolarus, Ted A; Saigal, Christopher S; Litwin, Mark S

2016-02-15

For certain men with low-risk prostate cancer, aggressive treatment results in marginal survival benefits while exposing them to urinary and sexual side effects. Nevertheless, expectant management has been underused. In the current study, the authors evaluated the association between various factors and expectant management use among veterans diagnosed with prostate cancer. The authors identified men diagnosed with prostate cancer in 2008. The outcome of interest was use of expectant management, based on documentation captured through an in-depth chart review. Multivariable regression models were fit to examine associations between use of expectant management and patient demographics, cancer severity, and facility characteristics. The authors assessed variation across 21 tertiary care regions and 52 facilities by generating predicted probabilities for receipt of expectant management. Expectant management was more common among patients aged ≥75 years (40% vs 27% for those aged < 55 years; odds ratio, 2.57) and those with low-risk tumors (49% vs 20% for patients with high-risk tumors; odds ratio, 5.35). There was no association noted between patient comorbidity and receipt of expectant management (P = .90). There were also no associations found between facility factors and use of expectant management (all P>.05). Among ideal candidates for expectant management, receipt of expectant management varied considerably across individual facilities (0%-85%; P<.001). Patient age and tumor risk were found to be more strongly associated with use of expectant management than patient comorbidity. Although use of expectant management appears broadly appropriate, there was variation in expectant management noted between hospitals that was apparently not attributable to facility factors. Research determining the basis of this variation, with a focus on providers, will be critical to help optimize prostate cancer treatment for veterans. © 2015 American Cancer Society.

12 CFR 1005.9 - Receipts at electronic terminals; periodic statements.

Code of Federal Regulations, 2012 CFR

2012-01-01

... TRANSFERS (REGULATION E) § 1005.9 Receipts at electronic terminals; periodic statements. (a) Receipts at... shall make a receipt available to a consumer at the time the consumer initiates an electronic fund transfer at an electronic terminal. The receipt shall set forth the following information, as applicable...

A System for the Semantic Multimodal Analysis of News Audio-Visual Content

NASA Astrophysics Data System (ADS)

Mezaris, Vasileios; Gidaros, Spyros; Papadopoulos, GeorgiosTh; Kasper, Walter; Steffen, Jörg; Ordelman, Roeland; Huijbregts, Marijn; de Jong, Franciska; Kompatsiaris, Ioannis; Strintzis, MichaelG

2010-12-01

News-related content is nowadays among the most popular types of content for users in everyday applications. Although the generation and distribution of news content has become commonplace, due to the availability of inexpensive media capturing devices and the development of media sharing services targeting both professional and user-generated news content, the automatic analysis and annotation that is required for supporting intelligent search and delivery of this content remains an open issue. In this paper, a complete architecture for knowledge-assisted multimodal analysis of news-related multimedia content is presented, along with its constituent components. The proposed analysis architecture employs state-of-the-art methods for the analysis of each individual modality (visual, audio, text) separately and proposes a novel fusion technique based on the particular characteristics of news-related content for the combination of the individual modality analysis results. Experimental results on news broadcast video illustrate the usefulness of the proposed techniques in the automatic generation of semantic annotations.

Multi-scale chromatin state annotation using a hierarchical hidden Markov model

NASA Astrophysics Data System (ADS)

Marco, Eugenio; Meuleman, Wouter; Huang, Jialiang; Glass, Kimberly; Pinello, Luca; Wang, Jianrong; Kellis, Manolis; Yuan, Guo-Cheng

2017-04-01

Chromatin-state analysis is widely applied in the studies of development and diseases. However, existing methods operate at a single length scale, and therefore cannot distinguish large domains from isolated elements of the same type. To overcome this limitation, we present a hierarchical hidden Markov model, diHMM, to systematically annotate chromatin states at multiple length scales. We apply diHMM to analyse a public ChIP-seq data set. diHMM not only accurately captures nucleosome-level information, but identifies domain-level states that vary in nucleosome-level state composition, spatial distribution and functionality. The domain-level states recapitulate known patterns such as super-enhancers, bivalent promoters and Polycomb repressed regions, and identify additional patterns whose biological functions are not yet characterized. By integrating chromatin-state information with gene expression and Hi-C data, we identify context-dependent functions of nucleosome-level states. Thus, diHMM provides a powerful tool for investigating the role of higher-order chromatin structure in gene regulation.

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes.

PubMed

Lowe, Todd M; Chan, Patricia P

2016-07-08

High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes. Newly developed tRNAscan-SE 2.0 has advanced the state-of-the-art methodology in tRNA gene detection and functional prediction, captured by rich new content of the companion Genomic tRNA Database. Previously, web-server tRNA detection was isolated from knowledge of existing tRNAs and their annotation. In this update of the tRNAscan-SE On-line resource, we tie together improvements in tRNA classification with greatly enhanced biological context via dynamically generated links between web server search results, the most relevant genes in the GtRNAdb and interactive, rich genome context provided by UCSC genome browsers. The tRNAscan-SE On-line web server can be accessed at http://trna.ucsc.edu/tRNAscan-SE/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Analysis of mammalian gene function through broad-based phenotypic screens across a consortium of mouse clinics.

PubMed

de Angelis, Martin Hrabě; Nicholson, George; Selloum, Mohammed; White, Jacqui; Morgan, Hugh; Ramirez-Solis, Ramiro; Sorg, Tania; Wells, Sara; Fuchs, Helmut; Fray, Martin; Adams, David J; Adams, Niels C; Adler, Thure; Aguilar-Pimentel, Antonio; Ali-Hadji, Dalila; Amann, Gregory; André, Philippe; Atkins, Sarah; Auburtin, Aurelie; Ayadi, Abdel; Becker, Julien; Becker, Lore; Bedu, Elodie; Bekeredjian, Raffi; Birling, Marie-Christine; Blake, Andrew; Bottomley, Joanna; Bowl, Mike; Brault, Véronique; Busch, Dirk H; Bussell, James N; Calzada-Wack, Julia; Cater, Heather; Champy, Marie-France; Charles, Philippe; Chevalier, Claire; Chiani, Francesco; Codner, Gemma F; Combe, Roy; Cox, Roger; Dalloneau, Emilie; Dierich, André; Di Fenza, Armida; Doe, Brendan; Duchon, Arnaud; Eickelberg, Oliver; Esapa, Chris T; El Fertak, Lahcen; Feigel, Tanja; Emelyanova, Irina; Estabel, Jeanne; Favor, Jack; Flenniken, Ann; Gambadoro, Alessia; Garrett, Lilian; Gates, Hilary; Gerdin, Anna-Karin; Gkoutos, George; Greenaway, Simon; Glasl, Lisa; Goetz, Patrice; Da Cruz, Isabelle Goncalves; Götz, Alexander; Graw, Jochen; Guimond, Alain; Hans, Wolfgang; Hicks, Geoff; Hölter, Sabine M; Höfler, Heinz; Hancock, John M; Hoehndorf, Robert; Hough, Tertius; Houghton, Richard; Hurt, Anja; Ivandic, Boris; Jacobs, Hughes; Jacquot, Sylvie; Jones, Nora; Karp, Natasha A; Katus, Hugo A; Kitchen, Sharon; Klein-Rodewald, Tanja; Klingenspor, Martin; Klopstock, Thomas; Lalanne, Valerie; Leblanc, Sophie; Lengger, Christoph; le Marchand, Elise; Ludwig, Tonia; Lux, Aline; McKerlie, Colin; Maier, Holger; Mandel, Jean-Louis; Marschall, Susan; Mark, Manuel; Melvin, David G; Meziane, Hamid; Micklich, Kateryna; Mittelhauser, Christophe; Monassier, Laurent; Moulaert, David; Muller, Stéphanie; Naton, Beatrix; Neff, Frauke; Nolan, Patrick M; Nutter, Lauryl Mj; Ollert, Markus; Pavlovic, Guillaume; Pellegata, Natalia S; Peter, Emilie; Petit-Demoulière, Benoit; Pickard, Amanda; Podrini, Christine; Potter, Paul; Pouilly, Laurent; Puk, Oliver; Richardson, David; Rousseau, Stephane; Quintanilla-Fend, Leticia; Quwailid, Mohamed M; Racz, Ildiko; Rathkolb, Birgit; Riet, Fabrice; Rossant, Janet; Roux, Michel; Rozman, Jan; Ryder, Ed; Salisbury, Jennifer; Santos, Luis; Schäble, Karl-Heinz; Schiller, Evelyn; Schrewe, Anja; Schulz, Holger; Steinkamp, Ralf; Simon, Michelle; Stewart, Michelle; Stöger, Claudia; Stöger, Tobias; Sun, Minxuan; Sunter, David; Teboul, Lydia; Tilly, Isabelle; Tocchini-Valentini, Glauco P; Tost, Monica; Treise, Irina; Vasseur, Laurent; Velot, Emilie; Vogt-Weisenhorn, Daniela; Wagner, Christelle; Walling, Alison; Weber, Bruno; Wendling, Olivia; Westerberg, Henrik; Willershäuser, Monja; Wolf, Eckhard; Wolter, Anne; Wood, Joe; Wurst, Wolfgang; Yildirim, Ali Önder; Zeh, Ramona; Zimmer, Andreas; Zimprich, Annemarie; Holmes, Chris; Steel, Karen P; Herault, Yann; Gailus-Durner, Valérie; Mallon, Ann-Marie; Brown, Steve Dm

2015-09-01

The function of the majority of genes in the mouse and human genomes remains unknown. The mouse embryonic stem cell knockout resource provides a basis for the characterization of relationships between genes and phenotypes. The EUMODIC consortium developed and validated robust methodologies for the broad-based phenotyping of knockouts through a pipeline comprising 20 disease-oriented platforms. We developed new statistical methods for pipeline design and data analysis aimed at detecting reproducible phenotypes with high power. We acquired phenotype data from 449 mutant alleles, representing 320 unique genes, of which half had no previous functional annotation. We captured data from over 27,000 mice, finding that 83% of the mutant lines are phenodeviant, with 65% demonstrating pleiotropy. Surprisingly, we found significant differences in phenotype annotation according to zygosity. New phenotypes were uncovered for many genes with previously unknown function, providing a powerful basis for hypothesis generation and further investigation in diverse systems.

Multi-label learning with fuzzy hypergraph regularization for protein subcellular location prediction.

PubMed

Chen, Jing; Tang, Yuan Yan; Chen, C L Philip; Fang, Bin; Lin, Yuewei; Shang, Zhaowei

2014-12-01

Protein subcellular location prediction aims to predict the location where a protein resides within a cell using computational methods. Considering the main limitations of the existing methods, we propose a hierarchical multi-label learning model FHML for both single-location proteins and multi-location proteins. The latent concepts are extracted through feature space decomposition and label space decomposition under the nonnegative data factorization framework. The extracted latent concepts are used as the codebook to indirectly connect the protein features to their annotations. We construct dual fuzzy hypergraphs to capture the intrinsic high-order relations embedded in not only feature space, but also label space. Finally, the subcellular location annotation information is propagated from the labeled proteins to the unlabeled proteins by performing dual fuzzy hypergraph Laplacian regularization. The experimental results on the six protein benchmark datasets demonstrate the superiority of our proposed method by comparing it with the state-of-the-art methods, and illustrate the benefit of exploiting both feature correlations and label correlations.

Expert knowledge maps for knowledge management: a case study in Traditional Chinese Medicine research.

PubMed

Cui, Meng; Yang, Shuo; Yu, Tong; Yang, Ce; Gao, Yonghong; Zhu, Haiyan

2013-10-01

To design a model to capture information on the state and trends of knowledge creation, at both an individual and an organizational level, in order to enhance knowledge management. We designed a graph-theoretic knowledge model, the expert knowledge map (EKM), based on literature-based annotation. A case study in the domain of Traditional Chinese Medicine research was used to illustrate the usefulness of the model. The EKM successfully captured various aspects of knowledge and enhanced knowledge management within the case-study organization through the provision of knowledge graphs, expert graphs, and expert-knowledge biography. Our model could help to reveal the hot topics, trends, and products of the research done by an organization. It can potentially be used to facilitate knowledge learning, sharing and decision-making among researchers, academicians, students, and administrators of organizations.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity.

PubMed

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-09-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. © 2015 The Authors Protein Science published by Wiley Periodicals, Inc. on behalf of The Protein Society.

Resolving protein structure-function-binding site relationships from a binding site similarity network perspective.

PubMed

Mudgal, Richa; Srinivasan, Narayanaswamy; Chandra, Nagasuma

2017-07-01

Functional annotation is seldom straightforward with complexities arising due to functional divergence in protein families or functional convergence between non-homologous protein families, leading to mis-annotations. An enzyme may contain multiple domains and not all domains may be involved in a given function, adding to the complexity in function annotation. To address this, we use binding site information from bound cognate ligands and catalytic residues, since it can help in resolving fold-function relationships at a finer level and with higher confidence. A comprehensive database of 2,020 fold-function-binding site relationships has been systematically generated. A network-based approach is employed to capture the complexity in these relationships, from which different types of associations are deciphered, that identify versatile protein folds performing diverse functions, same function associated with multiple folds and one-to-one relationships. Binding site similarity networks integrated with fold, function, and ligand similarity information are generated to understand the depth of these relationships. Apart from the observed continuity in the functional site space, network properties of these revealed versatile families with topologically different or dissimilar binding sites and structural families that perform very similar functions. As a case study, subtle changes in the active site of a set of evolutionarily related superfamilies are studied using these networks. Tracing of such similarities in evolutionarily related proteins provide clues into the transition and evolution of protein functions. Insights from this study will be helpful in accurate and reliable functional annotations of uncharacterized proteins, poly-pharmacology, and designing enzymes with new functional capabilities. Proteins 2017; 85:1319-1335. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Comparison of topological clustering within protein networks using edge metrics that evaluate full sequence, full structure, and active site microenvironment similarity

PubMed Central

Leuthaeuser, Janelle B; Knutson, Stacy T; Kumar, Kiran; Babbitt, Patricia C; Fetrow, Jacquelyn S

2015-01-01

The development of accurate protein function annotation methods has emerged as a major unsolved biological problem. Protein similarity networks, one approach to function annotation via annotation transfer, group proteins into similarity-based clusters. An underlying assumption is that the edge metric used to identify such clusters correlates with functional information. In this contribution, this assumption is evaluated by observing topologies in similarity networks using three different edge metrics: sequence (BLAST), structure (TM-Align), and active site similarity (active site profiling, implemented in DASP). Network topologies for four well-studied protein superfamilies (enolase, peroxiredoxin (Prx), glutathione transferase (GST), and crotonase) were compared with curated functional hierarchies and structure. As expected, network topology differs, depending on edge metric; comparison of topologies provides valuable information on structure/function relationships. Subnetworks based on active site similarity correlate with known functional hierarchies at a single edge threshold more often than sequence- or structure-based networks. Sequence- and structure-based networks are useful for identifying sequence and domain similarities and differences; therefore, it is important to consider the clustering goal before deciding appropriate edge metric. Further, conserved active site residues identified in enolase and GST active site subnetworks correspond with published functionally important residues. Extension of this analysis yields predictions of functionally determinant residues for GST subgroups. These results support the hypothesis that active site similarity-based networks reveal clusters that share functional details and lay the foundation for capturing functionally relevant hierarchies using an approach that is both automatable and can deliver greater precision in function annotation than current similarity-based methods. PMID:26073648

An information gathering system for medical image inspection

NASA Astrophysics Data System (ADS)

Lee, Young-Jin; Bajcsy, Peter

2005-04-01

We present an information gathering system for medical image inspection that consists of software tools for capturing computer-centric and human-centric information. Computer-centric information includes (1) static annotations, such as (a) image drawings enclosing any selected area, a set of areas with similar colors, a set of salient points, and (b) textual descriptions associated with either image drawings or links between pairs of image drawings, and (2) dynamic (or temporal) information, such as mouse movements, zoom level changes, image panning and frame selections from an image stack. Human-centric information is represented by video and audio signals that are acquired by computer-mounted cameras and microphones. The short-term goal of the presented system is to facilitate learning of medical novices from medical experts, while the long-term goal is to data mine all information about image inspection for assisting in making diagnoses. In this work, we built basic software functionality for gathering computer-centric and human-centric information of the aforementioned variables. Next, we developed the information playback capabilities of all gathered information for educational purposes. Finally, we prototyped text-based and image template-based search engines to retrieve information from recorded annotations, for example, (a) find all annotations containing the word "blood vessels", or (b) search for similar areas to a selected image area. The information gathering system for medical image inspection reported here has been tested with images from the Histology Atlas database.

TSSer: an automated method to identify transcription start sites in prokaryotic genomes from differential RNA sequencing data.

PubMed

Jorjani, Hadi; Zavolan, Mihaela

2014-04-01

Accurate identification of transcription start sites (TSSs) is an essential step in the analysis of transcription regulatory networks. In higher eukaryotes, the capped analysis of gene expression technology enabled comprehensive annotation of TSSs in genomes such as those of mice and humans. In bacteria, an equivalent approach, termed differential RNA sequencing (dRNA-seq), has recently been proposed, but the application of this approach to a large number of genomes is hindered by the paucity of computational analysis methods. With few exceptions, when the method has been used, annotation of TSSs has been largely done manually. In this work, we present a computational method called 'TSSer' that enables the automatic inference of TSSs from dRNA-seq data. The method rests on a probabilistic framework for identifying both genomic positions that are preferentially enriched in the dRNA-seq data as well as preferentially captured relative to neighboring genomic regions. Evaluating our approach for TSS calling on several publicly available datasets, we find that TSSer achieves high consistency with the curated lists of annotated TSSs, but identifies many additional TSSs. Therefore, TSSer can accelerate genome-wide identification of TSSs in bacterial genomes and can aid in further characterization of bacterial transcription regulatory networks. TSSer is freely available under GPL license at http://www.clipz.unibas.ch/TSSer/index.php

L'archivage a long terme de la maquette numerique trois-dimensionnelle annotee

NASA Astrophysics Data System (ADS)

Kheddouci, Fawzi

The use of engineering drawings in the development of mechanical products, including the exchange of engineering data as well as for archiving, is common industry practice. Traditionally, paper has been the mean to deliver those needs. However, these practices have evolved in favour of computerized tools and methods for the creation, diffusion and preservation of data involved in the process of developing aeronautical products characterized by life cycles that can exceed 70 years. Therefore, it is necessary to redefine how to maintain this data in a context whereby engineering drawings are being replaced by the 3D annotated digital mock-up. This thesis addresses the issue of long-term archiving of 3D annotated digital mock-ups, which includes geometric and dimensional tolerances, as well as other notes and specifications, in compliance with the requirements formulated by the aviation industry including regulatory and legal requirements. First, we review the requirements imposed by the aviation industry in the context of long-term archiving of 3D annotated digital mock-ups. We then consider alternative solutions. We begin by identifying the theoretical approach behind the choice of a conceptual model for digital long-term archiving. Then we evaluate, among the proposed alternatives, an archiving format that will guarantee the preservation of the integrity of the 3D annotated model (geometry, tolerances and other metadata) and its sustainability. The evaluation of 3D PDF PRC as a potential archiving format is carried out on a sample of 185 3D CATIA V5 models (parts and assemblies) provided by industrial partners. This evaluation is guided by a set of criteria including the transfer of geometry, 3D annotations, views, captures and parts positioning in assembly. The results indicate that maintaining the exact geometry is done successfully when transferring CATIA V5 models to 3D PDF PRC. Concerning the transfer of 3D annotations, we observed degradation associated with their display on the 3D model. This problem can, however, be solved by performing the conversion of the native model to STEP first, and then to 3D PDF PRC. In view of current tools, PDF 3D PRC is considered as a potential solution for long-term archiving of 3D annotated models for individual parts. However, this solution is currently not deemed adequate for archiving assemblies. The practice of 2D drawing will thus remain, in the short term, for assemblies.

System for detecting special nuclear materials

DOEpatents

Jandel, Marian; Rusev, Gencho Yordanov; Taddeucci, Terry Nicholas

2015-07-14

The present disclosure includes a radiological material detector having a convertor material that emits one or more photons in response to a capture of a neutron emitted by a radiological material; a photon detector arranged around the convertor material and that produces an electrical signal in response to a receipt of a photon; and a processor connected to the photon detector, the processor configured to determine the presence of a radiological material in response to a predetermined signature of the electrical signal produced at the photon detector. One or more detectors described herein can be integrated into a detection system that is suited for use in port monitoring, treaty compliance, and radiological material management activities.

The evolution of ovule number and flower size in wind-pollinated plants.

PubMed

Friedman, Jannice; Barrett, Spencer C H

2011-02-01

In angiosperms, ovules are "packaged" within individual flowers, and an optimal strategy should occur depending on pollination and resource conditions. In animal-pollinated species, wide variation in ovule number per flower occurs, and this contrasts with wind-pollinated plants, where most species possess uniovulate flowers. This pattern is usually explained as an adaptive response to low pollen receipt in wind-pollinated species. Here, we develop a phenotypic model for the evolution of ovule number per flower that incorporates the aerodynamics of pollen capture and a fixed resource pool for provisioning of flowers, ovules, and seeds. Our results challenge the prevailing explanation for the association between uniovulate flowers and wind pollination. We demonstrate that when flowers are small and inexpensive, as they are in wind-pollinated species, ovule number should be minimized and lower than the average number of pollen tubes per style, even under stochastic pollination and fertilization regimes. The model predicts that plants benefit from producing many small inexpensive flowers, even though some flowers capture too few pollen grains to fertilize their ovules. Wind-pollinated plants with numerous flowers distributed throughout the inflorescence, each with a single ovule or a few ovules, sample more of the airstream, and this should maximize pollen capture and seed production.

7 CFR 735.303 - Electronic warehouse receipts.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Electronic warehouse receipts. 735.303 Section 735.303... AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Receipts § 735.303 Electronic warehouse receipts. (a) Warehouse operators issuing EWR under the Act may issue EWR...

7 CFR 735.303 - Electronic warehouse receipts.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 7 2011-01-01 2011-01-01 false Electronic warehouse receipts. 735.303 Section 735.303... AGRICULTURE REGULATIONS FOR WAREHOUSES REGULATIONS FOR THE UNITED STATES WAREHOUSE ACT Warehouse Receipts § 735.303 Electronic warehouse receipts. (a) Warehouse operators issuing EWR under the Act may issue EWR...

48 CFR 315.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 4 2013-10-01 2013-10-01 false Exchanges with industry before receipt of proposals. 315.201 Section 315.201 Federal Acquisition Regulations System HEALTH AND... Receipt of Proposals and Information 315.201 Exchanges with industry before receipt of proposals. (e)(1...

48 CFR 1415.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false Exchanges with industry before receipt of proposals. 1415.201 Section 1415.201 Federal Acquisition Regulations System DEPARTMENT... Receipt of Proposals and Information 1415.201 Exchanges with industry before receipt of proposals. (a) Use...

48 CFR 1415.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false Exchanges with industry before receipt of proposals. 1415.201 Section 1415.201 Federal Acquisition Regulations System DEPARTMENT... Receipt of Proposals and Information 1415.201 Exchanges with industry before receipt of proposals. (a) Use...

48 CFR 315.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 4 2012-10-01 2012-10-01 false Exchanges with industry before receipt of proposals. 315.201 Section 315.201 Federal Acquisition Regulations System HEALTH AND... Receipt of Proposals and Information 315.201 Exchanges with industry before receipt of proposals. (e)(1...

48 CFR 1415.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false Exchanges with industry before receipt of proposals. 1415.201 Section 1415.201 Federal Acquisition Regulations System DEPARTMENT... Receipt of Proposals and Information 1415.201 Exchanges with industry before receipt of proposals. (a) Use...

48 CFR 315.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 4 2014-10-01 2014-10-01 false Exchanges with industry before receipt of proposals. 315.201 Section 315.201 Federal Acquisition Regulations System HEALTH AND... Receipt of Proposals and Information 315.201 Exchanges with industry before receipt of proposals. (e)(1...

48 CFR 315.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 4 2011-10-01 2011-10-01 false Exchanges with industry before receipt of proposals. 315.201 Section 315.201 Federal Acquisition Regulations System HEALTH AND... Receipt of Proposals and Information 315.201 Exchanges with industry before receipt of proposals. (e)(1...

48 CFR 1415.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false Exchanges with industry before receipt of proposals. 1415.201 Section 1415.201 Federal Acquisition Regulations System DEPARTMENT... Receipt of Proposals and Information 1415.201 Exchanges with industry before receipt of proposals. (a) Use...

48 CFR 1415.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Exchanges with industry before receipt of proposals. 1415.201 Section 1415.201 Federal Acquisition Regulations System DEPARTMENT... Receipt of Proposals and Information 1415.201 Exchanges with industry before receipt of proposals. (a) Use...

76 FR 40749 - Agency Information Collection Activities: Records and Supporting Data: Importation, Receipt...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-07-11

...] Agency Information Collection Activities: Records and Supporting Data: Importation, Receipt, Storage, and... collection. (2) Title of the Form/Collection: Records and Supporting Data: Importation, Receipt, Storage, and... importation, manufacture, receipt, storage, and disposition of all explosive materials covered under 18 U.S.C...

7 CFR 735.302 - Paper warehouse receipts.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Paper warehouse receipts. 735.302 Section 735.302... § 735.302 Paper warehouse receipts. Paper warehouse receipts must be issued as follows: (a) On distinctive paper specified by DACO; (b) Printed by a printer authorized by DACO; and (c) Issued, identified...

7 CFR 735.302 - Paper warehouse receipts.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 7 2011-01-01 2011-01-01 false Paper warehouse receipts. 735.302 Section 735.302... § 735.302 Paper warehouse receipts. Paper warehouse receipts must be issued as follows: (a) On distinctive paper specified by DACO; (b) Printed by a printer authorized by DACO; and (c) Issued, identified...

12 CFR 205.9 - Receipts at electronic terminals; periodic statements.

Code of Federal Regulations, 2011 CFR

2011-01-01

... RESERVE SYSTEM ELECTRONIC FUND TRANSFERS (REGULATION E) § 205.9 Receipts at electronic terminals; periodic..., a financial institution shall make a receipt available to a consumer at the time the consumer initiates an electronic fund transfer at an electronic terminal. The receipt shall set forth the following...

12 CFR 205.9 - Receipts at electronic terminals; periodic statements.

Code of Federal Regulations, 2013 CFR

2013-01-01

... RESERVE SYSTEM ELECTRONIC FUND TRANSFERS (REGULATION E) § 205.9 Receipts at electronic terminals; periodic..., a financial institution shall make a receipt available to a consumer at the time the consumer initiates an electronic fund transfer at an electronic terminal. The receipt shall set forth the following...

12 CFR 1005.9 - Receipts at electronic terminals; periodic statements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... TRANSFERS (REGULATION E) General § 1005.9 Receipts at electronic terminals; periodic statements. (a... institution shall make a receipt available to a consumer at the time the consumer initiates an electronic fund transfer at an electronic terminal. The receipt shall set forth the following information, as applicable...

12 CFR 205.9 - Receipts at electronic terminals; periodic statements.

Code of Federal Regulations, 2014 CFR

2014-01-01

... RESERVE SYSTEM ELECTRONIC FUND TRANSFERS (REGULATION E) § 205.9 Receipts at electronic terminals; periodic..., a financial institution shall make a receipt available to a consumer at the time the consumer initiates an electronic fund transfer at an electronic terminal. The receipt shall set forth the following...

12 CFR 205.9 - Receipts at electronic terminals; periodic statements.

Code of Federal Regulations, 2010 CFR

2010-01-01

... RESERVE SYSTEM ELECTRONIC FUND TRANSFERS (REGULATION E) § 205.9 Receipts at electronic terminals; periodic..., a financial institution shall make a receipt available to a consumer at the time the consumer initiates an electronic fund transfer at an electronic terminal. The receipt shall set forth the following...

12 CFR 205.9 - Receipts at electronic terminals; periodic statements.

Code of Federal Regulations, 2012 CFR

2012-01-01

... RESERVE SYSTEM ELECTRONIC FUND TRANSFERS (REGULATION E) § 205.9 Receipts at electronic terminals; periodic..., a financial institution shall make a receipt available to a consumer at the time the consumer initiates an electronic fund transfer at an electronic terminal. The receipt shall set forth the following...

12 CFR 1005.9 - Receipts at electronic terminals; periodic statements.

Code of Federal Regulations, 2013 CFR

2013-01-01

... TRANSFERS (REGULATION E) General § 1005.9 Receipts at electronic terminals; periodic statements. (a... institution shall make a receipt available to a consumer at the time the consumer initiates an electronic fund transfer at an electronic terminal. The receipt shall set forth the following information, as applicable...

5 CFR 843.206 - Designation of beneficiary-proof of receipt.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Designation of beneficiary-proof of receipt. 843.206 Section 843.206 Administrative Personnel OFFICE OF PERSONNEL MANAGEMENT (CONTINUED) CIVIL... One-time Payments § 843.206 Designation of beneficiary—proof of receipt. (a) Upon receipt of a...

17 CFR 31.8 - Cover of leverage contracts.

Code of Federal Regulations, 2011 CFR

2011-04-01

... this section. (2) Permissible cover for a long leverage contract is limited to: (i) Warehouse receipts... and accrued interest on any loan against such warehouse receipts does not exceed 70 percent of the current market value of the commodity represented by each receipt. (ii) Warehouse receipts for gold...

27 CFR 28.251 - Railway express receipts.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Railway express receipts... § 28.251 Railway express receipts. Where the exportation is to a contiguous foreign country and the shipment is by railway express, a receipt issued by the railway express agency may be accepted in lieu of...

40 CFR 725.29 - EPA acknowledgement of receipt of submission.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false EPA acknowledgement of receipt of... Procedures § 725.29 EPA acknowledgement of receipt of submission. (a) EPA will acknowledge receipt of each... Toxics Document Control Officer. (b) The acknowledgement does not constitute a finding by EPA that the...

27 CFR 28.290 - Receipt in foreign trade zone.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Receipt in foreign trade zone. 28.290 Section 28.290 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE... in Foreign-Trade Zone § 28.290 Receipt in foreign trade zone. On receipt at the zone, the shipment...

27 CFR 28.290 - Receipt in foreign trade zone.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Receipt in foreign trade zone. 28.290 Section 28.290 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE... in Foreign-Trade Zone § 28.290 Receipt in foreign trade zone. On receipt at the zone, the shipment...

27 CFR 28.290 - Receipt in foreign trade zone.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Receipt in foreign trade zone. 28.290 Section 28.290 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE... in Foreign-Trade Zone § 28.290 Receipt in foreign trade zone. On receipt at the zone, the shipment...

27 CFR 28.290 - Receipt in foreign trade zone.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Receipt in foreign trade zone. 28.290 Section 28.290 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE... in Foreign-Trade Zone § 28.290 Receipt in foreign trade zone. On receipt at the zone, the shipment...

48 CFR 915.201 - Exchanges with industry before receipt of proposals. (DOE coverage-paragraph (e)).

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 5 2010-10-01 2010-10-01 false Exchanges with industry before receipt of proposals. (DOE coverage-paragraph (e)). 915.201 Section 915.201 Federal Acquisition... Solicitation and Receipt of Proposals and Information 915.201 Exchanges with industry before receipt of...

Methods used to address fidelity of receipt in health intervention research: a citation analysis and systematic review.

PubMed

Rixon, Lorna; Baron, Justine; McGale, Nadine; Lorencatto, Fabiana; Francis, Jill; Davies, Anna

2016-11-18

The American Behaviour Change Consortium (BCC) framework acknowledges patients as active participants and supports the need to investigate the fidelity with which they receive interventions, i.e. receipt. According to this framework, addressing receipt consists in using strategies to assess or enhance participants' understanding and/or performance of intervention skills. This systematic review aims to establish the frequency with which receipt is addressed as defined in the BCC framework in health research, and to describe the methods used in papers informed by the BCC framework and in the wider literature. A forward citation search on papers presenting the BCC framework was performed to determine the frequency with which receipt as defined in this framework was addressed. A second electronic database search, including search terms pertaining to fidelity, receipt, health and process evaluations was performed to identify papers reporting on receipt in the wider literature and irrespective of the framework used. These results were combined with forward citation search results to review methods to assess receipt. Eligibility criteria and data extraction forms were developed and applied to papers. Results are described in a narrative synthesis. 19.6% of 33 studies identified from the forward citation search to report on fidelity were found to address receipt. In 60.6% of these, receipt was assessed in relation to understanding and in 42.4% in relation to performance of skill. Strategies to enhance these were present in 12.1% and 21.1% of studies, respectively. Fifty-five studies were included in the review of the wider literature. Several frameworks and operationalisations of receipt were reported, but the latter were not always consistent with the guiding framework. Receipt was most frequently operationalised in relation to intervention content (16.4%), satisfaction (14.5%), engagement (14.5%), and attendance (14.5%). The majority of studies (90.0%) included subjective assessments of receipt. These relied on quantitative (76.0%) rather than qualitative (42.0%) methods and studies collected data on intervention recipients (50.0%), intervention deliverers (28.0%), or both (22.0%). Few studies (26.0%) reported on the reliability or validity of methods used. Receipt is infrequently addressed in health research and improvements to methods of assessment and reporting are required.

Australian sea-floor survey data, with images and expert annotations.

PubMed

Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Marzinelli, Ezequiel M; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B

2015-01-01

This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research.

Australian sea-floor survey data, with images and expert annotations

PubMed Central

Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B.

2015-01-01

This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research. PMID:26528396

Australian sea-floor survey data, with images and expert annotations

NASA Astrophysics Data System (ADS)

Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B.

2015-10-01

This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typically spend several minutes on each of thousands of images, labeling substratum type and biota at a subset of points. Labels from four Australian research groups were combined using the CATAMI classification scheme, a hierarchical classification scheme based on taxonomy and morphology for scoring marine imagery. This data set consists of 407,968 expert labeled points from around the Australian coast, with associated images, geolocation and other sensor data. The robotic surveys that collected this data form part of Australia's Integrated Marine Observing System (IMOS) ongoing benthic monitoring program. There is reuse potential in marine science, robotics, and computer vision research.

Draft genome of the gayal, Bos frontalis

PubMed Central

Wang, Ming-Shan; Zeng, Yan; Wang, Xiao; Nie, Wen-Hui; Wang, Jin-Huan; Su, Wei-Ting; Xiong, Zi-Jun; Wang, Sheng; Qu, Kai-Xing; Yan, Shou-Qing; Yang, Min-Min; Wang, Wen; Dong, Yang; Zhang, Ya-Ping

2017-01-01

Abstract Gayal (Bos frontalis), also known as mithan or mithun, is a large endangered semi-domesticated bovine that has a limited geographical distribution in the hill-forests of China, Northeast India, Bangladesh, Myanmar, and Bhutan. Many questions about the gayal such as its origin, population history, and genetic basis of local adaptation remain largely unresolved. De novo sequencing and assembly of the whole gayal genome provides an opportunity to address these issues. We report a high-depth sequencing, de novo assembly, and annotation of a female Chinese gayal genome. Based on the Illumina genomic sequencing platform, we have generated 350.38 Gb of raw data from 16 different insert-size libraries. A total of 276.86 Gb of clean data is retained after quality control. The assembled genome is about 2.85 Gb with scaffold and contig N50 sizes of 2.74 Mb and 14.41 kb, respectively. Repetitive elements account for 48.13% of the genome. Gene annotation has yielded 26 667 protein-coding genes, of which 97.18% have been functionally annotated. BUSCO assessment shows that our assembly captures 93% (3183 of 4104) of the core eukaryotic genes and 83.1% of vertebrate universal single-copy orthologs. We provide the first comprehensive de novo genome of the gayal. This genetic resource is integral for investigating the origin of the gayal and performing comparative genomic studies to improve understanding of the speciation and divergence of bovine species. The assembled genome could be used as reference in future population genetic studies of gayal. PMID:29048483

7 CFR 1.13 - Date of receipt of requests or appeals.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 1 2013-01-01 2013-01-01 false Date of receipt of requests or appeals. 1.13 Section 1.13 Agriculture Office of the Secretary of Agriculture ADMINISTRATIVE REGULATIONS Official Records § 1.13 Date of receipt of requests or appeals. The date of receipt of a request or appeal shall be the...

15 CFR 768.8 - Eligibility of expedited licensing procedures for non-controlled countries.

Code of Federal Regulations, 2010 CFR

2010-01-01

... FAS; or (3) On receipt of a TAC certification. (c) Upon initiation of an eligibility evaluation following receipt of either a FAS or TAC certification, BIS will notify the claimant or TAC of the receipt... Secretary considers relevant. (f) Within 30 days of the receipt of the FAS or TAC certification, BIS will...

15 CFR 768.8 - Eligibility of expedited licensing procedures for non-controlled countries.

Code of Federal Regulations, 2011 CFR

2011-01-01

... FAS; or (3) On receipt of a TAC certification. (c) Upon initiation of an eligibility evaluation following receipt of either a FAS or TAC certification, BIS will notify the claimant or TAC of the receipt... Secretary considers relevant. (f) Within 30 days of the receipt of the FAS or TAC certification, BIS will...

15 CFR 768.8 - Eligibility of expedited licensing procedures for non-controlled countries.

Code of Federal Regulations, 2012 CFR

2012-01-01

... FAS; or (3) On receipt of a TAC certification. (c) Upon initiation of an eligibility evaluation following receipt of either a FAS or TAC certification, BIS will notify the claimant or TAC of the receipt... Secretary considers relevant. (f) Within 30 days of the receipt of the FAS or TAC certification, BIS will...

15 CFR 768.8 - Eligibility of expedited licensing procedures for non-controlled countries.

Code of Federal Regulations, 2014 CFR

2014-01-01

... FAS; or (3) On receipt of a TAC certification. (c) Upon initiation of an eligibility evaluation following receipt of either a FAS or TAC certification, BIS will notify the claimant or TAC of the receipt... Secretary considers relevant. (f) Within 30 days of the receipt of the FAS or TAC certification, BIS will...

15 CFR 768.8 - Eligibility of expedited licensing procedures for non-controlled countries.

Code of Federal Regulations, 2013 CFR

2013-01-01

... FAS; or (3) On receipt of a TAC certification. (c) Upon initiation of an eligibility evaluation following receipt of either a FAS or TAC certification, BIS will notify the claimant or TAC of the receipt... Secretary considers relevant. (f) Within 30 days of the receipt of the FAS or TAC certification, BIS will...

Implant vendors and hospitals: competing influences over product choice by orthopedic surgeons.

PubMed

Burns, Lawton R; Housman, Michael G; Booth, Robert E; Koenig, Aaron

2009-01-01

Vendors of hip and knee implants court orthopedic surgeons to adopt their products. Hospitals, which have to pay for these products, now court the same surgeons to help reduce the number of vendors and contain implant costs. This study measures the surgeon's perceived alignment of interests with both vendors and hospitals and gauges surgeons' exposure and receptivity to hospital cost-containment efforts. We surveyed all practicing orthopedists performing 12 or more implant procedures annually in Pennsylvania. The survey identified the surgeon's preferred vendor, tenure with that vendor, use of the vendor during residency training, receipt of financial payments from the vendor, alignment of interests with both vendor and hospital stakeholders, and exposure and receptivity to hospital cost-containment efforts. Surgeons have long-standing relationships with implant vendors, but only a small proportion receive financial payments. Surgeons align most closely with the vendor's sales representative and least closely with the hospital's purchasing manager. Paradoxically, surgeons support hospital efforts to limit the number of vendors but report that their own choice of vendor is not constrained. The major drivers of surgeons' alignment and stance toward cost containment are their tenure with and receipt of financial payments from the vendor. Hospitals face a competitive disadvantage in capturing the attention of orthopedists, compared with implant vendors. The vendors' advantage stems from historical, financial, and service benefits offered to surgeons. Hospital executives now seek to offer comparable benefits to surgeons.

High vulnerability to household food insecurity in a sample of Canadian renter households in government-subsidized housing.

PubMed

Fafard St-Germain, Andrée-Anne; Tarasuk, Valerie

2017-06-16

To determine the prevalence and severity of household food insecurity and examine household material circumstances related to food insecurity in a sample of renter households in government-subsidized housing. Cross-sectional data from the 2010 Survey of Household Spending were used to determine the food insecurity status of 455 renter households living in the 10 provinces and receiving a government housing subsidy. Multivariable logistic regressions were conducted to examine the relationship between household characteristics describing material circumstances and food insecurity. One in two households was food insecure. Marginal, moderate and severe food insecurity affected 9.0%, 23.3% and 18.5% of households respectively. Household economic resources, as captured with after-tax income, after-rent income, or total expenditure, had an independent, inverse relationship with food insecurity. Among the other characteristics examined, more adults or children in the household, presence of a member with disability, and receipt of social assistance increased the odds of food insecurity, but receipt of social assistance lost statistical significance when controlling for total expenditure. Presence of a senior in the household was independently associated with lower odds of food insecurity. Our findings suggest that more effective income-based interventions are needed to address food insecurity among low-income households receiving government housing subsidies. A better integration of housing and income-based policies is necessary to support household food security among government-subsidized renter households.

The Impact of Receipt of an Employee Pension on the Psychological Well-Being of Retired Persons.

ERIC Educational Resources Information Center

Thompson, Gayle B.

This analysis of the relationship between receipt of an employee pension and happiness among retired men and women suggests that the relationship is the result of the effect of pension receipt on total income, as well as other variables which impact on or are related in a noncasual way to pension receipt. It appears that there is nothing intrinsic…

The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

PubMed Central

2013-01-01

Background The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community. PMID:24093723

OVAS: an open-source variant analysis suite with inheritance modelling.

PubMed

Mozere, Monika; Tekman, Mehmet; Kari, Jameela; Bockenhauer, Detlef; Kleta, Robert; Stanescu, Horia

2018-02-08

The advent of modern high-throughput genetics continually broadens the gap between the rising volume of sequencing data, and the tools required to process them. The need to pinpoint a small subset of functionally important variants has now shifted towards identifying the critical differences between normal variants and disease-causing ones. The ever-increasing reliance on cloud-based services for sequence analysis and the non-transparent methods they utilize has prompted the need for more in-situ services that can provide a safer and more accessible environment to process patient data, especially in circumstances where continuous internet usage is limited. To address these issues, we herein propose our standalone Open-source Variant Analysis Sequencing (OVAS) pipeline; consisting of three key stages of processing that pertain to the separate modes of annotation, filtering, and interpretation. Core annotation performs variant-mapping to gene-isoforms at the exon/intron level, append functional data pertaining the type of variant mutation, and determine hetero/homozygosity. An extensive inheritance-modelling module in conjunction with 11 other filtering components can be used in sequence ranging from single quality control to multi-file penetrance model specifics such as X-linked recessive or mosaicism. Depending on the type of interpretation required, additional annotation is performed to identify organ specificity through gene expression and protein domains. In the course of this paper we analysed an autosomal recessive case study. OVAS made effective use of the filtering modules to recapitulate the results of the study by identifying the prescribed compound-heterozygous disease pattern from exome-capture sequence input samples. OVAS is an offline open-source modular-driven analysis environment designed to annotate and extract useful variants from Variant Call Format (VCF) files, and process them under an inheritance context through a top-down filtering schema of swappable modules, run entirely off a live bootable medium and accessed locally through a web-browser.

HPIDB 2.0: a curated database for host–pathogen interactions

PubMed Central

Ammari, Mais G.; Gresham, Cathy R.; McCarthy, Fiona M.; Nanduri, Bindu

2016-01-01

Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural host–pathogen systems. Therefore, resources that annotate, predict and display the HPI that underpin infectious diseases are critical for developing novel intervention strategies. HPIDB 2.0 (http://www.agbase.msstate.edu/hpi/main.html) is a resource for HPI data, and contains 45, 238 manually curated entries in the current release. Since the first description of the database in 2010, multiple enhancements to HPIDB data and interface services were made that are described here. Notably, HPIDB 2.0 now provides targeted biocuration of molecular interaction data. As a member of the International Molecular Exchange consortium, annotations provided by HPIDB 2.0 curators meet community standards to provide detailed contextual experimental information and facilitate data sharing. Moreover, HPIDB 2.0 provides access to rapidly available community annotations that capture minimum molecular interaction information to address immediate researcher needs for HPI network analysis. In addition to curation, HPIDB 2.0 integrates HPI from existing external sources and contains tools to infer additional HPI where annotated data are scarce. Compared to other interaction databases, our data collection approach ensures HPIDB 2.0 users access the most comprehensive HPI data from a wide range of pathogens and their hosts (594 pathogen and 70 host species, as of February 2016). Improvements also include enhanced search capacity, addition of Gene Ontology functional information, and implementation of network visualization. The changes made to HPIDB 2.0 content and interface ensure that users, especially agricultural researchers, are able to easily access and analyse high quality, comprehensive HPI data. All HPIDB 2.0 data are updated regularly, are publically available for direct download, and are disseminated to other molecular interaction resources. Database URL: http://www.agbase.msstate.edu/hpi/main.html PMID:27374121

Frequent ice cream consumption is associated with reduced striatal response to receipt of an ice cream–based milkshake123

PubMed Central

Stice, Eric

2012-01-01

Background: Weight gain leads to reduced reward-region responsivity to energy-dense food receipt, and consumption of an energy-dense diet compared with an isocaloric, low-energy-density diet leads to reduced dopamine receptors. Furthermore, phasic dopamine signaling to palatable food receipt decreases after repeated intake of that food, which collectively suggests that frequent intake of an energy-dense food may reduce striatal response to receipt of that food. Objective: We tested the hypothesis that frequent ice cream consumption would be associated with reduced activation in reward-related brain regions (eg, striatum) in response to receipt of an ice cream–based milkshake and examined the influence of adipose tissue and the specificity of this relation. Design: Healthy-weight adolescents (n = 151) underwent fMRI during receipt of a milkshake and during receipt of a tasteless solution. Percentage body fat, reported food intake, and food craving and liking were assessed. Results: Milkshake receipt robustly activated the striatal regions, yet frequent ice cream consumption was associated with a reduced response to milkshake receipt in these reward-related brain regions. Percentage body fat, total energy intake, percentage of energy from fat and sugar, and intake of other energy-dense foods were not related to the neural response to milkshake receipt. Conclusions: Our results provide novel evidence that frequent consumption of ice cream, independent of body fat, is related to a reduction in reward-region responsivity in humans, paralleling the tolerance observed in drug addiction. Data also imply that intake of a particular energy-dense food results in attenuated reward-region responsivity specifically to that food, which suggests that sensory aspects of eating and reward learning may drive the specificity. PMID:22338036

Frequent ice cream consumption is associated with reduced striatal response to receipt of an ice cream-based milkshake.

PubMed

Burger, Kyle S; Stice, Eric

2012-04-01

Weight gain leads to reduced reward-region responsivity to energy-dense food receipt, and consumption of an energy-dense diet compared with an isocaloric, low-energy-density diet leads to reduced dopamine receptors. Furthermore, phasic dopamine signaling to palatable food receipt decreases after repeated intake of that food, which collectively suggests that frequent intake of an energy-dense food may reduce striatal response to receipt of that food. We tested the hypothesis that frequent ice cream consumption would be associated with reduced activation in reward-related brain regions (eg, striatum) in response to receipt of an ice cream-based milkshake and examined the influence of adipose tissue and the specificity of this relation. Healthy-weight adolescents (n = 151) underwent fMRI during receipt of a milkshake and during receipt of a tasteless solution. Percentage body fat, reported food intake, and food craving and liking were assessed. Milkshake receipt robustly activated the striatal regions, yet frequent ice cream consumption was associated with a reduced response to milkshake receipt in these reward-related brain regions. Percentage body fat, total energy intake, percentage of energy from fat and sugar, and intake of other energy-dense foods were not related to the neural response to milkshake receipt. Our results provide novel evidence that frequent consumption of ice cream, independent of body fat, is related to a reduction in reward-region responsivity in humans, paralleling the tolerance observed in drug addiction. Data also imply that intake of a particular energy-dense food results in attenuated reward-region responsivity specifically to that food, which suggests that sensory aspects of eating and reward learning may drive the specificity.

Modular biological function is most effectively captured by combining molecular interaction data types.

PubMed

Ames, Ryan M; Macpherson, Jamie I; Pinney, John W; Lovell, Simon C; Robertson, David L

2013-01-01

Large-scale molecular interaction data sets have the potential to provide a comprehensive, system-wide understanding of biological function. Although individual molecules can be promiscuous in terms of their contribution to function, molecular functions emerge from the specific interactions of molecules giving rise to modular organisation. As functions often derive from a range of mechanisms, we demonstrate that they are best studied using networks derived from different sources. Implementing a graph partitioning algorithm we identify subnetworks in yeast protein-protein interaction (PPI), genetic interaction and gene co-regulation networks. Among these subnetworks we identify cohesive subgraphs that we expect to represent functional modules in the different data types. We demonstrate significant overlap between the subgraphs generated from the different data types and show these overlaps can represent related functions as represented by the Gene Ontology (GO). Next, we investigate the correspondence between our subgraphs and the Gene Ontology. This revealed varying degrees of coverage of the biological process, molecular function and cellular component ontologies, dependent on the data type. For example, subgraphs from the PPI show enrichment for 84%, 58% and 93% of annotated GO terms, respectively. Integrating the interaction data into a combined network increases the coverage of GO. Furthermore, the different annotation types of GO are not predominantly associated with one of the interaction data types. Collectively our results demonstrate that successful capture of functional relationships by network data depends on both the specific biological function being characterised and the type of network data being used. We identify functions that require integrated information to be accurately represented, demonstrating the limitations of individual data types. Combining interaction subnetworks across data types is therefore essential for fully understanding the complex and emergent nature of biological function.

Increasing Receipt of Women's Preventive Services

PubMed Central

Fox, Jared

2015-01-01

Abstract The receipt of clinical preventive services is important for health promotion and prevention of illness, death, and disability for women in the United States. Today, the Affordable Care Act makes a variety of evidence-based preventive services available with no out-of-pocket cost to women with certain health insurance plans. Nevertheless, available service receipt data suggest receipt of the services for all American adults remains suboptimal. This article seeks to raise awareness about the critical gaps in the delivery of preventive services to women and highlight opportunities for women, primary care providers, and public health professionals to increase receipt of clinical preventive services among women. PMID:26447836

Household income differences in food sources and food items purchased.

PubMed

French, Simone A; Wall, Melanie; Mitchell, Nathan R

2010-10-26

The present study examined income-related household food purchases among a sample of 90 households from the community. Annotated food purchase receipts were collected for a four-week period by the primary household shopper. Receipt food source and foods items were classified into specific categories, and food quantities in ounces were recorded by research staff. For home sources, a limited number of food/beverage categories were recorded. For eating out sources, all food/beverage items were recorded. Median monthly per person dollars spent and per person ounces purchased were computed. Food sources and food categories were examined by household income tertile. A community-based sample of 90 households. Higher income households spent significantly more dollars per person per month from both home and eating out sources compared with lower income households ($163 versus $100, p < .001). Compared with lower income households, higher income households spent significantly more home source dollars on both fruits/vegetables (21.5 versus 10.2, p < .001) and sweets/snacks (17.3 versus 8.3, p < .001), but did not differ on home dollars spent on sugar sweetened beverages (2.0 versus 1.7, p < .46). The proportion of home beverages that were sugar sweetened beverages was significantly higher among lower income households (45% versus 26%, p < .01). Within eating out sources, lower income households spent a significantly greater percent of dollars per person at carry out places (54% versus 37%, p < .01). No income differences were observed for dollars spent at discount grocery stores, small grocery stores or convenience stores. Higher income households spent more money on both healthy and less healthy foods from a wide range of sources. Lower income households spent a larger proportion of their eating out dollars at carry out places, and a larger proportion of their home beverage purchases were sugar sweetened beverages.

19 CFR 162.15 - Receipt for seized property.

Code of Federal Regulations, 2014 CFR

2014-04-01

.... A receipt for property seized under a search warrant shall be left with the person in charge or possession of the premises, or in the absence of any person, the receipt shall be left in some conspicuous...

19 CFR 162.15 - Receipt for seized property.

Code of Federal Regulations, 2013 CFR

2013-04-01

.... A receipt for property seized under a search warrant shall be left with the person in charge or possession of the premises, or in the absence of any person, the receipt shall be left in some conspicuous...

19 CFR 162.15 - Receipt for seized property.

Code of Federal Regulations, 2012 CFR

2012-04-01

.... A receipt for property seized under a search warrant shall be left with the person in charge or possession of the premises, or in the absence of any person, the receipt shall be left in some conspicuous...

19 CFR 162.15 - Receipt for seized property.

Code of Federal Regulations, 2011 CFR

2011-04-01

.... A receipt for property seized under a search warrant shall be left with the person in charge or possession of the premises, or in the absence of any person, the receipt shall be left in some conspicuous...

Validating self-reported food expenditures against food store and eating-out receipts.

PubMed

Tang, W; Aggarwal, A; Liu, Z; Acheson, M; Rehm, C D; Moudon, A V; Drewnowski, A

2016-03-01

To compare objective food store and eating-out receipts with self-reported household food expenditures. The Seattle Obesity Study II was based on a representative sample of King County adults, Washington, USA. Self-reported household food expenditures were modeled on the Flexible Consumer Behavior Survey (FCBS) Module from 2007 to 2009 National Health and Nutrition Examination Survey (NHANES). Objective food expenditure data were collected using receipts. Self-reported food expenditures for 447 participants were compared with receipts using paired t-tests, Bland-Altman plots and κ-statistics. Bias by sociodemographics was also examined. Self-reported expenditures closely matched with objective receipt data. Paired t-tests showed no significant differences between receipts and self-reported data on total food expenditures, expenditures at food stores or eating out. However, the highest-income strata showed weaker agreement. Bland-Altman plots confirmed no significant bias across both methods-mean difference: 6.4; agreement limits: -123.5 to 143.4 for total food expenditures, mean difference 5.7 for food stores and mean difference 1.7 for eating out. The κ-statistics showed good agreement for each (κ 0.51, 0.41 and 0.49 respectively. Households with higher education and income had significantly more number of receipts and higher food expenditures. Self-reported food expenditures using NHANES questions, both for food stores and eating out, serve as a decent proxy for objective household food expenditures from receipts. This method should be used with caution among high-income populations, or with high food expenditures. This is the first validation of the FCBS food expenditures question using food store and eating-out receipts.

Seabird databases and the new paradigm for scientific publication and attribution

USGS Publications Warehouse

Hatch, Scott A.

2010-01-01

For more than 300 years, the peer-reviewed journal article has been the principal medium for packaging and delivering scientific data. With new tools for managing digital data, a new paradigm is emerging—one that demands open and direct access to data and that enables and rewards a broad-based approach to scientific questions. Ground-breaking papers in the future will increasingly be those that creatively mine and synthesize vast stores of data available on the Internet. This is especially true for conservation science, in which essential data can be readily captured in standard record formats. For seabird professionals, a number of globally shared databases are in the offing, or should be. These databases will capture the salient results of inventories and monitoring, pelagic surveys, diet studies, and telemetry. A number of real or perceived barriers to data sharing exist, but none is insurmountable. Our discipline should take an important stride now by adopting a specially designed markup language for annotating and sharing seabird data.

17 CFR 31.12 - Segregation.

Code of Federal Regulations, 2010 CFR

2010-04-01

... United States, or unencumbered warehouse receipts for inventory held in approved contract market..., and proceeds from any sale, liquidation or other disposition of obligations or warehouse receipts... to purchase obligations or warehouse receipts of the type described in this paragraph (b) shall...

17 CFR 31.12 - Segregation.

Code of Federal Regulations, 2011 CFR

2011-04-01

... United States, or unencumbered warehouse receipts for inventory held in approved contract market..., and proceeds from any sale, liquidation or other disposition of obligations or warehouse receipts... to purchase obligations or warehouse receipts of the type described in this paragraph (b) shall...

ePIANNO: ePIgenomics ANNOtation tool.

PubMed

Liu, Chia-Hsin; Ho, Bing-Ching; Chen, Chun-Ling; Chang, Ya-Hsuan; Hsu, Yi-Chiung; Li, Yu-Cheng; Yuan, Shin-Sheng; Huang, Yi-Huan; Chang, Chi-Sheng; Li, Ker-Chau; Chen, Hsuan-Yu

2016-01-01

Recently, with the development of next generation sequencing (NGS), the combination of chromatin immunoprecipitation (ChIP) and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html). ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project) and gene-disease association information of GWAS (NHGRI) with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics) data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies.

Draft genome of the leopard gecko, Eublepharis macularius.

PubMed

Xiong, Zijun; Li, Fang; Li, Qiye; Zhou, Long; Gamble, Tony; Zheng, Jiao; Kui, Ling; Li, Cai; Li, Shengbin; Yang, Huanming; Zhang, Guojie

2016-10-26

Geckos are among the most species-rich reptile groups and the sister clade to all other lizards and snakes. Geckos possess a suite of distinctive characteristics, including adhesive digits, nocturnal activity, hard, calcareous eggshells, and a lack of eyelids. However, one gecko clade, the Eublepharidae, appears to be the exception to most of these 'rules' and lacks adhesive toe pads, has eyelids, and lays eggs with soft, leathery eggshells. These differences make eublepharids an important component of any investigation into the underlying genomic innovations contributing to the distinctive phenotypes in 'typical' geckos. We report high-depth genome sequencing, assembly, and annotation for a male leopard gecko, Eublepharis macularius (Eublepharidae). Illumina sequence data were generated from seven insert libraries (ranging from 170 to 20 kb), representing a raw sequencing depth of 136X from 303 Gb of data, reduced to 84X and 187 Gb after filtering. The assembled genome of 2.02 Gb was close to the 2.23 Gb estimated by k-mer analysis. Scaffold and contig N50 sizes of 664 and 20 kb, respectively, were comparable to the previously published Gekko japonicus genome. Repetitive elements accounted for 42 % of the genome. Gene annotation yielded 24,755 protein-coding genes, of which 93 % were functionally annotated. CEGMA and BUSCO assessment showed that our assembly captured 91 % (225 of 248) of the core eukaryotic genes, and 76 % of vertebrate universal single-copy orthologs. Assembly of the leopard gecko genome provides a valuable resource for future comparative genomic studies of geckos and other squamate reptiles.

Computational analyses of spectral trees from electrospray multi-stage mass spectrometry to aid metabolite identification.

PubMed

Cao, Mingshu; Fraser, Karl; Rasmussen, Susanne

2013-10-31

Mass spectrometry coupled with chromatography has become the major technical platform in metabolomics. Aided by peak detection algorithms, the detected signals are characterized by mass-over-charge ratio (m/z) and retention time. Chemical identities often remain elusive for the majority of the signals. Multi-stage mass spectrometry based on electrospray ionization (ESI) allows collision-induced dissociation (CID) fragmentation of selected precursor ions. These fragment ions can assist in structural inference for metabolites of low molecular weight. Computational investigations of fragmentation spectra have increasingly received attention in metabolomics and various public databases house such data. We have developed an R package "iontree" that can capture, store and analyze MS2 and MS3 mass spectral data from high throughput metabolomics experiments. The package includes functions for ion tree construction, an algorithm (distMS2) for MS2 spectral comparison, and tools for building platform-independent ion tree (MS2/MS3) libraries. We have demonstrated the utilization of the package for the systematic analysis and annotation of fragmentation spectra collected in various metabolomics platforms, including direct infusion mass spectrometry, and liquid chromatography coupled with either low resolution or high resolution mass spectrometry. Assisted by the developed computational tools, we have demonstrated that spectral trees can provide informative evidence complementary to retention time and accurate mass to aid with annotating unknown peaks. These experimental spectral trees once subjected to a quality control process, can be used for querying public MS2 databases or de novo interpretation. The putatively annotated spectral trees can be readily incorporated into reference libraries for routine identification of metabolites.

Sequencing analysis of 20,000 full-length cDNA clones from cassava reveals lineage specific expansions in gene families related to stress response

PubMed Central

Sakurai, Tetsuya; Plata, Germán; Rodríguez-Zapata, Fausto; Seki, Motoaki; Salcedo, Andrés; Toyoda, Atsushi; Ishiwata, Atsushi; Tohme, Joe; Sakaki, Yoshiyuki; Shinozaki, Kazuo; Ishitani, Manabu

2007-01-01

Background Cassava, an allotetraploid known for its remarkable tolerance to abiotic stresses is an important source of energy for humans and animals and a raw material for many industrial processes. A full-length cDNA library of cassava plants under normal, heat, drought, aluminum and post harvest physiological deterioration conditions was built; 19968 clones were sequence-characterized using expressed sequence tags (ESTs). Results The ESTs were assembled into 6355 contigs and 9026 singletons that were further grouped into 10577 scaffolds; we found 4621 new cassava sequences and 1521 sequences with no significant similarity to plant protein databases. Transcripts of 7796 distinct genes were captured and we were able to assign a functional classification to 78% of them while finding more than half of the enzymes annotated in metabolic pathways in Arabidopsis. The annotation of sequences that were not paired to transcripts of other species included many stress-related functional categories showing that our library is enriched with stress-induced genes. Finally, we detected 230 putative gene duplications that include key enzymes in reactive oxygen species signaling pathways and could play a role in cassava stress response features. Conclusion The cassava full-length cDNA library here presented contains transcripts of genes involved in stress response as well as genes important for different areas of cassava research. This library will be an important resource for gene discovery, characterization and cloning; in the near future it will aid the annotation of the cassava genome. PMID:18096061

Semi-automatic semantic annotation of PubMed Queries: a study on quality, efficiency, satisfaction

PubMed Central

Névéol, Aurélie; Islamaj-Doğan, Rezarta; Lu, Zhiyong

2010-01-01

Information processing algorithms require significant amounts of annotated data for training and testing. The availability of such data is often hindered by the complexity and high cost of production. In this paper, we investigate the benefits of a state-of-the-art tool to help with the semantic annotation of a large set of biomedical information queries. Seven annotators were recruited to annotate a set of 10,000 PubMed® queries with 16 biomedical and bibliographic categories. About half of the queries were annotated from scratch, while the other half were automatically pre-annotated and manually corrected. The impact of the automatic pre-annotations was assessed on several aspects of the task: time, number of actions, annotator satisfaction, inter-annotator agreement, quality and number of the resulting annotations. The analysis of annotation results showed that the number of required hand annotations is 28.9% less when using pre-annotated results from automatic tools. As a result, the overall annotation time was substantially lower when pre-annotations were used, while inter-annotator agreement was significantly higher. In addition, there was no statistically significant difference in the semantic distribution or number of annotations produced when pre-annotations were used. The annotated query corpus is freely available to the research community. This study shows that automatic pre-annotations are found helpful by most annotators. Our experience suggests using an automatic tool to assist large-scale manual annotation projects. This helps speed-up the annotation time and improve annotation consistency while maintaining high quality of the final annotations. PMID:21094696

On combining image-based and ontological semantic dissimilarities for medical image retrieval applications

PubMed Central

Kurtz, Camille; Depeursinge, Adrien; Napel, Sandy; Beaulieu, Christopher F.; Rubin, Daniel L.

2014-01-01

Computer-assisted image retrieval applications can assist radiologists by identifying similar images in archives as a means to providing decision support. In the classical case, images are described using low-level features extracted from their contents, and an appropriate distance is used to find the best matches in the feature space. However, using low-level image features to fully capture the visual appearance of diseases is challenging and the semantic gap between these features and the high-level visual concepts in radiology may impair the system performance. To deal with this issue, the use of semantic terms to provide high-level descriptions of radiological image contents has recently been advocated. Nevertheless, most of the existing semantic image retrieval strategies are limited by two factors: they require manual annotation of the images using semantic terms and they ignore the intrinsic visual and semantic relationships between these annotations during the comparison of the images. Based on these considerations, we propose an image retrieval framework based on semantic features that relies on two main strategies: (1) automatic “soft” prediction of ontological terms that describe the image contents from multi-scale Riesz wavelets and (2) retrieval of similar images by evaluating the similarity between their annotations using a new term dissimilarity measure, which takes into account both image-based and ontological term relations. The combination of these strategies provides a means of accurately retrieving similar images in databases based on image annotations and can be considered as a potential solution to the semantic gap problem. We validated this approach in the context of the retrieval of liver lesions from computed tomographic (CT) images and annotated with semantic terms of the RadLex ontology. The relevance of the retrieval results was assessed using two protocols: evaluation relative to a dissimilarity reference standard defined for pairs of images on a 25-images dataset, and evaluation relative to the diagnoses of the retrieved images on a 72-images dataset. A normalized discounted cumulative gain (NDCG) score of more than 0.92 was obtained with the first protocol, while AUC scores of more than 0.77 were obtained with the second protocol. This automatical approach could provide real-time decision support to radiologists by showing them similar images with associated diagnoses and, where available, responses to therapies. PMID:25036769

Assisted annotation of medical free text using RapTAT

PubMed Central

Gobbel, Glenn T; Garvin, Jennifer; Reeves, Ruth; Cronin, Robert M; Heavirland, Julia; Williams, Jenifer; Weaver, Allison; Jayaramaraja, Shrimalini; Giuse, Dario; Speroff, Theodore; Brown, Steven H; Xu, Hua; Matheny, Michael E

2014-01-01

Objective To determine whether assisted annotation using interactive training can reduce the time required to annotate a clinical document corpus without introducing bias. Materials and methods A tool, RapTAT, was designed to assist annotation by iteratively pre-annotating probable phrases of interest within a document, presenting the annotations to a reviewer for correction, and then using the corrected annotations for further machine learning-based training before pre-annotating subsequent documents. Annotators reviewed 404 clinical notes either manually or using RapTAT assistance for concepts related to quality of care during heart failure treatment. Notes were divided into 20 batches of 19–21 documents for iterative annotation and training. Results The number of correct RapTAT pre-annotations increased significantly and annotation time per batch decreased by ∼50% over the course of annotation. Annotation rate increased from batch to batch for assisted but not manual reviewers. Pre-annotation F-measure increased from 0.5 to 0.6 to >0.80 (relative to both assisted reviewer and reference annotations) over the first three batches and more slowly thereafter. Overall inter-annotator agreement was significantly higher between RapTAT-assisted reviewers (0.89) than between manual reviewers (0.85). Discussion The tool reduced workload by decreasing the number of annotations needing to be added and helping reviewers to annotate at an increased rate. Agreement between the pre-annotations and reference standard, and agreement between the pre-annotations and assisted annotations, were similar throughout the annotation process, which suggests that pre-annotation did not introduce bias. Conclusions Pre-annotations generated by a tool capable of interactive training can reduce the time required to create an annotated document corpus by up to 50%. PMID:24431336

31 CFR 362.1 - Declaration of “valuables”.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) Securities and other instruments or documents, private and public. Abstracts of title. Assignments. Bills... receipts. Voting trust receipts. Warehouse receipts. Warrants. And other instruments or documents similar... and collections of artistic, historical, scientific or educational value which are the property of the...

31 CFR 362.1 - Declaration of “valuables”.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) Securities and other instruments or documents, private and public. Abstracts of title. Assignments. Bills... receipts. Voting trust receipts. Warehouse receipts. Warrants. And other instruments or documents similar... and collections of artistic, historical, scientific or educational value which are the property of the...

31 CFR 362.1 - Declaration of “valuables”.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) Securities and other instruments or documents, private and public. Abstracts of title. Assignments. Bills... receipts. Voting trust receipts. Warehouse receipts. Warrants. And other instruments or documents similar... and collections of artistic, historical, scientific or educational value which are the property of the...

31 CFR 362.1 - Declaration of “valuables”.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) Securities and other instruments or documents, private and public. Abstracts of title. Assignments. Bills... receipts. Voting trust receipts. Warehouse receipts. Warrants. And other instruments or documents similar... and collections of artistic, historical, scientific or educational value which are the property of the...

Global Network Alignment in the Context of Aging.

PubMed

Faisal, Fazle Elahi; Zhao, Han; Milenkovic, Tijana

2015-01-01

Analogous to sequence alignment, network alignment (NA) can be used to transfer biological knowledge across species between conserved network regions. NA faces two algorithmic challenges: 1) Which cost function to use to capture "similarities" between nodes in different networks? 2) Which alignment strategy to use to rapidly identify "high-scoring" alignments from all possible alignments? We "break down" existing state-of-the-art methods that use both different cost functions and different alignment strategies to evaluate each combination of their cost functions and alignment strategies. We find that a combination of the cost function of one method and the alignment strategy of another method beats the existing methods. Hence, we propose this combination as a novel superior NA method. Then, since human aging is hard to study experimentally due to long lifespan, we use NA to transfer aging-related knowledge from well annotated model species to poorly annotated human. By doing so, we produce novel human aging-related knowledge, which complements currently available knowledge about aging that has been obtained mainly by sequence alignment. We demonstrate significant similarity between topological and functional properties of our novel predictions and those of known aging-related genes. We are the first to use NA to learn more about aging.

Effectiveness of image features and similarity measures in cluster-based approaches for content-based image retrieval

NASA Astrophysics Data System (ADS)

Du, Hongbo; Al-Jubouri, Hanan; Sellahewa, Harin

2014-05-01

Content-based image retrieval is an automatic process of retrieving images according to image visual contents instead of textual annotations. It has many areas of application from automatic image annotation and archive, image classification and categorization to homeland security and law enforcement. The key issues affecting the performance of such retrieval systems include sensible image features that can effectively capture the right amount of visual contents and suitable similarity measures to find similar and relevant images ranked in a meaningful order. Many different approaches, methods and techniques have been developed as a result of very intensive research in the past two decades. Among many existing approaches, is a cluster-based approach where clustering methods are used to group local feature descriptors into homogeneous regions, and search is conducted by comparing the regions of the query image against those of the stored images. This paper serves as a review of works in this area. The paper will first summarize the existing work reported in the literature and then present the authors' own investigations in this field. The paper intends to highlight not only achievements made by recent research but also challenges and difficulties still remaining in this area.

Shared periodic performer movements coordinate interactions in duo improvisations.

PubMed

Eerola, Tuomas; Jakubowski, Kelly; Moran, Nikki; Keller, Peter E; Clayton, Martin

2018-02-01

Human interaction involves the exchange of temporally coordinated, multimodal cues. Our work focused on interaction in the visual domain, using music performance as a case for analysis due to its temporally diverse and hierarchical structures. We made use of two improvising duo datasets-(i) performances of a jazz standard with a regular pulse and (ii) non-pulsed, free improvizations-to investigate whether human judgements of moments of interaction between co-performers are influenced by body movement coordination at multiple timescales. Bouts of interaction in the performances were manually annotated by experts and the performers' movements were quantified using computer vision techniques. The annotated interaction bouts were then predicted using several quantitative movement and audio features. Over 80% of the interaction bouts were successfully predicted by a broadband measure of the energy of the cross-wavelet transform of the co-performers' movements in non-pulsed duos. A more complex model, with multiple predictors that captured more specific, interacting features of the movements, was needed to explain a significant amount of variance in the pulsed duos. The methods developed here have key implications for future work on measuring visual coordination in musical ensemble performances, and can be easily adapted to other musical contexts, ensemble types and traditions.

Validating self-reported food expenditures against food store and eating-out receipts

PubMed Central

Tang, Wesley; Aggarwal, Anju; Liu, Zhongyuan; Acheson, Molly; Rehm, Colin D; Moudon, Anne Vernez; Drewnowski, Adam

2015-01-01

Objectives To compare objective food store and eating-out receipts with self-reported household food expenditures. Design and setting The Seattle Obesity Study (SOS II) was based on a representative sample of King County adults, Washington, USA. Self-reported household food expenditures were modeled on the Flexible Consumer Behavior Survey (FCBS) Module from 2007–2009 National Health and Nutrition Examination Survey (NHANES). Objective food expenditure data were collected using receipts. Self-reported food expenditures for 447 participants were compared to receipts using paired t-tests, Bland-Altman plots, and kappa statistics. Bias by socio-demographics was also examined. Results Self-reported expenditures closely matched with objective receipt data. Paired t-tests showed no significant differences between receipts and self-reported data on total food expenditures, expenditures at food stores, or eating out. However, the highest income strata showed weaker agreement. Bland Altman plots confirmed no significant bias across both methods - mean difference: 6.4; agreement limits: −123.5, 143.4 for total food expenditures, mean difference 5.7 for food stores, and mean difference 1.7 for eating-out. Kappa statistics showed good agreement for each (kappa 0.51, 0.41 and 0.49 respectively. Households with higher education and income had significantly more number of receipts and higher food expenditures. Conclusion Self-reported food expenditures using NHANES questions, both for food stores and eating-out, serve as a decent proxy for objective household food expenditures from receipts. This method should be used with caution among high income populations, or with high food expenditures. This is the first validation of the FCBS food expenditures question using food store and eating-out receipts. PMID:26486299

1 CFR 17.1 - Receipt and processing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 1 General Provisions 1 2011-01-01 2011-01-01 false Receipt and processing. 17.1 Section 17.1 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER PREPARATION, TRANSMITTAL, AND PROCESSING OF DOCUMENTS FILING FOR PUBLIC INSPECTION AND PUBLICATION SCHEDULES Receipt and Processing § 17.1...

1 CFR 17.1 - Receipt and processing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 1 General Provisions 1 2010-01-01 2010-01-01 false Receipt and processing. 17.1 Section 17.1 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER PREPARATION, TRANSMITTAL, AND PROCESSING OF DOCUMENTS FILING FOR PUBLIC INSPECTION AND PUBLICATION SCHEDULES Receipt and Processing § 17.1...

26 CFR 1.993-1 - Definition of qualified export receipts.

Code of Federal Regulations, 2013 CFR

2013-04-01

... this section. (h) Engineering and architectural services—(1) In general. Qualified export receipts of a DISC include gross receipts from engineering services (as described in subparagraph (5) of this... within or without the United States. (2) Services included. Engineering and architectural services...

26 CFR 1.993-1 - Definition of qualified export receipts.

Code of Federal Regulations, 2012 CFR

2012-04-01

... this section. (h) Engineering and architectural services—(1) In general. Qualified export receipts of a DISC include gross receipts from engineering services (as described in subparagraph (5) of this... within or without the United States. (2) Services included. Engineering and architectural services...

26 CFR 1.993-1 - Definition of qualified export receipts.

Code of Federal Regulations, 2011 CFR

2011-04-01

... this section. (h) Engineering and architectural services—(1) In general. Qualified export receipts of a DISC include gross receipts from engineering services (as described in subparagraph (5) of this... within or without the United States. (2) Services included. Engineering and architectural services...

26 CFR 1.993-1 - Definition of qualified export receipts.

Code of Federal Regulations, 2014 CFR

2014-04-01

... this section. (h) Engineering and architectural services—(1) In general. Qualified export receipts of a DISC include gross receipts from engineering services (as described in subparagraph (5) of this... within or without the United States. (2) Services included. Engineering and architectural services...

1 CFR 17.1 - Receipt and processing.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 1 General Provisions 1 2012-01-01 2012-01-01 false Receipt and processing. 17.1 Section 17.1 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER PREPARATION, TRANSMITTAL, AND PROCESSING OF DOCUMENTS FILING FOR PUBLIC INSPECTION AND PUBLICATION SCHEDULES Receipt and Processing § 17.1...

1 CFR 17.1 - Receipt and processing.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 1 General Provisions 1 2014-01-01 2012-01-01 true Receipt and processing. 17.1 Section 17.1 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER PREPARATION, TRANSMITTAL, AND PROCESSING OF DOCUMENTS FILING FOR PUBLIC INSPECTION AND PUBLICATION SCHEDULES Receipt and Processing § 17.1...

1 CFR 17.1 - Receipt and processing.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 1 General Provisions 1 2013-01-01 2012-01-01 true Receipt and processing. 17.1 Section 17.1 General Provisions ADMINISTRATIVE COMMITTEE OF THE FEDERAL REGISTER PREPARATION, TRANSMITTAL, AND PROCESSING OF DOCUMENTS FILING FOR PUBLIC INSPECTION AND PUBLICATION SCHEDULES Receipt and Processing § 17.1...

maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination.

PubMed

Hancock, David; Wilson, Michael; Velarde, Giles; Morrison, Norman; Hayes, Andrew; Hulme, Helen; Wood, A Joseph; Nashar, Karim; Kell, Douglas B; Brass, Andy

2005-11-03

maxdLoad2 is a relational database schema and Java application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: the flexibility of the meta-data that can be captured, the tools provided for importing data from spreadsheets and other tabular representations, the tools provided for the automatic creation of structured documents, the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file) can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention.maxdBrowse is hosted on a web-server and presents multiple interfaces to the contents of maxd databases. maxdBrowse emulates many of the browse and search features available in the maxdLoad2 application via a web-browser. This allows users who are not familiar with maxdLoad2 to browse and export microarray data from the database for their own analysis. The same browse and search features are also available via command-line and SOAP server interfaces. This both enables scripting of data export for use embedded in data repositories and analysis environments, and allows access to the maxd databases via web-service architectures. maxdLoad2 http://www.bioinf.man.ac.uk/microarray/maxd/ and maxdBrowse http://dbk.ch.umist.ac.uk/maxdBrowse are portable and compatible with all common operating systems and major database servers. They provide a powerful, flexible package for annotation of microarray experiments and a convenient dissemination environment. They are available for download and open sourced under the Artistic License.

6 CFR 29.6 - Acknowledgment of receipt, validation, and marking.

Code of Federal Regulations, 2010 CFR

2010-01-01

... PROTECTED CRITICAL INFRASTRUCTURE INFORMATION § 29.6 Acknowledgment of receipt, validation, and marking. (a... Program Manager's designees. (e) Validation of information. (1) The PCII Program Manager shall be... 6 Domestic Security 1 2010-01-01 2010-01-01 false Acknowledgment of receipt, validation, and...

7 CFR 735.303 - Electronic warehouse receipts.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 7 2013-01-01 2013-01-01 false Electronic warehouse receipts. 735.303 Section 735.303 Agriculture Regulations of the Department of Agriculture (Continued) FARM SERVICE AGENCY, DEPARTMENT OF... § 735.303 Electronic warehouse receipts. (a) Warehouse operators issuing EWR under the Act may issue EWR...

7 CFR 735.303 - Electronic warehouse receipts.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 7 2014-01-01 2014-01-01 false Electronic warehouse receipts. 735.303 Section 735.303 Agriculture Regulations of the Department of Agriculture (Continued) FARM SERVICE AGENCY, DEPARTMENT OF... § 735.303 Electronic warehouse receipts. (a) Warehouse operators issuing EWR under the Act may issue EWR...

7 CFR 735.303 - Electronic warehouse receipts.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 7 2012-01-01 2012-01-01 false Electronic warehouse receipts. 735.303 Section 735.303 Agriculture Regulations of the Department of Agriculture (Continued) FARM SERVICE AGENCY, DEPARTMENT OF... § 735.303 Electronic warehouse receipts. (a) Warehouse operators issuing EWR under the Act may issue EWR...

48 CFR 801.603-71 - Representatives of contracting officers; receipt of equipment, supplies, and nonpersonal services.

Code of Federal Regulations, 2010 CFR

2010-10-01

... contracting officers; receipt of equipment, supplies, and nonpersonal services. 801.603-71 Section 801.603-71... AFFAIRS ACQUISITION REGULATION SYSTEM Career Development, Contracting Authority, and Responsibilities 801.603-71 Representatives of contracting officers; receipt of equipment, supplies, and nonpersonal...

76 FR 69730 - Pesticide Products; Receipt of Applications to Register New Uses

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-09

... ENVIRONMENTAL PROTECTION AGENCY [EPA-HQ-OPP-2011-0005; FRL-9326-6] Pesticide Products; Receipt of... notice announces receipt of applications to register new uses for pesticide products containing currently... on-line instructions for submitting comments. Mail: Office of Pesticide Programs (OPP) Regulatory...

6 CFR 29.6 - Acknowledgment of receipt, validation, and marking.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 6 Domestic Security 1 2011-01-01 2011-01-01 false Acknowledgment of receipt, validation, and... PROTECTED CRITICAL INFRASTRUCTURE INFORMATION § 29.6 Acknowledgment of receipt, validation, and marking. (a... Program Manager's designees. (e) Validation of information. (1) The PCII Program Manager shall be...

6 CFR 29.6 - Acknowledgment of receipt, validation, and marking.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 6 Domestic Security 1 2012-01-01 2012-01-01 false Acknowledgment of receipt, validation, and... PROTECTED CRITICAL INFRASTRUCTURE INFORMATION § 29.6 Acknowledgment of receipt, validation, and marking. (a... Program Manager's designees. (e) Validation of information. (1) The PCII Program Manager shall be...

6 CFR 29.6 - Acknowledgment of receipt, validation, and marking.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 6 Domestic Security 1 2013-01-01 2013-01-01 false Acknowledgment of receipt, validation, and... PROTECTED CRITICAL INFRASTRUCTURE INFORMATION § 29.6 Acknowledgment of receipt, validation, and marking. (a... Program Manager's designees. (e) Validation of information. (1) The PCII Program Manager shall be...

6 CFR 29.6 - Acknowledgment of receipt, validation, and marking.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 6 Domestic Security 1 2014-01-01 2014-01-01 false Acknowledgment of receipt, validation, and... PROTECTED CRITICAL INFRASTRUCTURE INFORMATION § 29.6 Acknowledgment of receipt, validation, and marking. (a... Program Manager's designees. (e) Validation of information. (1) The PCII Program Manager shall be...

7 CFR 1427.11 - Warehouse receipts.

Code of Federal Regulations, 2010 CFR

2010-01-01

... (Signature or initials), Date. (3) Alterations in other inserted data on a machine card type warehouse... 7 Agriculture 10 2010-01-01 2010-01-01 false Warehouse receipts. 1427.11 Section 1427.11... Deficiency Payments § 1427.11 Warehouse receipts. (a) Producers may obtain loans on eligible cotton...

7 CFR 1427.11 - Warehouse receipts.

Code of Federal Regulations, 2011 CFR

2011-01-01

... (Signature or initials), Date. (3) Alterations in other inserted data on a machine card type warehouse... 7 Agriculture 10 2011-01-01 2011-01-01 false Warehouse receipts. 1427.11 Section 1427.11... Deficiency Payments § 1427.11 Warehouse receipts. (a) Producers may obtain loans on eligible cotton...

20 CFR 410.520 - Reductions; receipt of State benefit.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 20 Employees' Benefits 2 2010-04-01 2010-04-01 false Reductions; receipt of State benefit. 410.520 Section 410.520 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL COAL MINE HEALTH AND SAFETY ACT OF 1969, TITLE IV-BLACK LUNG BENEFITS (1969- ) Payment of Benefits § 410.520 Reductions; receipt of...

20 CFR 410.520 - Reductions; receipt of State benefit.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 20 Employees' Benefits 2 2011-04-01 2011-04-01 false Reductions; receipt of State benefit. 410.520 Section 410.520 Employees' Benefits SOCIAL SECURITY ADMINISTRATION FEDERAL COAL MINE HEALTH AND SAFETY ACT OF 1969, TITLE IV-BLACK LUNG BENEFITS (1969- ) Payment of Benefits § 410.520 Reductions; receipt of...

26 CFR 1.993-6 - Definition of gross receipts.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 10 2010-04-01 2010-04-01 false Definition of gross receipts. 1.993-6 Section 1.993-6 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Domestic International Sales Corporations § 1.993-6 Definition of gross receipts. (a...

26 CFR 1.924(a)-1T - Temporary regulations; definition of foreign trading gross receipts.

Code of Federal Regulations, 2014 CFR

2014-04-01

...) Engineering and architectural services—(1) In general. Foreign trading gross receipts of a FSC include gross receipts from engineering services (as described in paragraph (e)(5) of this section) or architectural... without the United States. (2) Services included. Engineering and architectural services include...

26 CFR 1.924(a)-1T - Temporary regulations; definition of foreign trading gross receipts.

Code of Federal Regulations, 2012 CFR

2012-04-01

...) Engineering and architectural services—(1) In general. Foreign trading gross receipts of a FSC include gross receipts from engineering services (as described in paragraph (e)(5) of this section) or architectural... without the United States. (2) Services included. Engineering and architectural services include...

26 CFR 1.924(a)-1T - Temporary regulations; definition of foreign trading gross receipts.

Code of Federal Regulations, 2013 CFR

2013-04-01

...) Engineering and architectural services—(1) In general. Foreign trading gross receipts of a FSC include gross receipts from engineering services (as described in paragraph (e)(5) of this section) or architectural... without the United States. (2) Services included. Engineering and architectural services include...

26 CFR 1.924(a)-1T - Temporary regulations; definition of foreign trading gross receipts.

Code of Federal Regulations, 2011 CFR

2011-04-01

...) Engineering and architectural services—(1) In general. Foreign trading gross receipts of a FSC include gross receipts from engineering services (as described in paragraph (e)(5) of this section) or architectural... without the United States. (2) Services included. Engineering and architectural services include...

48 CFR 315.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 4 2010-10-01 2010-10-01 false Exchanges with industry... Receipt of Proposals and Information 315.201 Exchanges with industry before receipt of proposals. (e)(1... complex projects involving R & D, IT, construction, and other highly technical requirements. An RFI may...

76 FR 82039 - Receipt of Petition for Decision That Nonconforming 2000-2003 Kawasaki ZR750 Motorcycles Are...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-29

... DEPARTMENT OF TRANSPORTATION National Highway Traffic Safety Administration [Docket No. NHTSA-2011... Motorcycles Are Eligible for Importation AGENCY: National Highway Traffic Safety Administration, DOT. ACTION: Receipt of petition. SUMMARY: This document announces receipt by the National Highway Traffic Safety...

78 FR 21945 - Notice of Receipt of Pesticide Products; Registration Applications To Register New Uses

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-12

... ENVIRONMENTAL PROTECTION AGENCY [EPA-HQ-OPP-2013-0025; FRL-9383-7] Notice of Receipt of Pesticide...). ACTION: Notice. SUMMARY: This notice announces receipt of applications to register new uses for pesticide... mail. Mail correspondence to the Registration Division (7505P), Office of Pesticide Programs...

77 FR 13599 - Pesticide Products; Receipt of Applications To Register New Uses

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-07

... ENVIRONMENTAL PROTECTION AGENCY [EPA-HQ-OPP-2012-0012; FRL-9337-6] Pesticide Products; Receipt of... notice announces receipt of applications to register new uses for pesticide products containing currently... instructions for submitting comments. Mail: Office of Pesticide Programs (OPP) Regulatory Public Docket (7502P...

45 CFR 1801.16 - Closing date for receipt of nominations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 45 Public Welfare 4 2012-10-01 2012-10-01 false Closing date for receipt of nominations. 1801.16 Section 1801.16 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.16 Closing date for receipt of...

45 CFR 1801.16 - Closing date for receipt of nominations.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 45 Public Welfare 4 2013-10-01 2013-10-01 false Closing date for receipt of nominations. 1801.16 Section 1801.16 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.16 Closing date for receipt of...

45 CFR 1801.16 - Closing date for receipt of nominations.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 45 Public Welfare 4 2011-10-01 2011-10-01 false Closing date for receipt of nominations. 1801.16 Section 1801.16 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.16 Closing date for receipt of...

45 CFR 1801.16 - Closing date for receipt of nominations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 4 2010-10-01 2010-10-01 false Closing date for receipt of nominations. 1801.16 Section 1801.16 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.16 Closing date for receipt of...

45 CFR 1801.16 - Closing date for receipt of nominations.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 45 Public Welfare 4 2014-10-01 2014-10-01 false Closing date for receipt of nominations. 1801.16 Section 1801.16 Public Welfare Regulations Relating to Public Welfare (Continued) HARRY S. TRUMAN SCHOLARSHIP FOUNDATION HARRY S. TRUMAN SCHOLARSHIP PROGRAM Nominations § 1801.16 Closing date for receipt of...

77 FR 61600 - Certain New Chemicals; Receipt and Status Information

Federal Register 2010, 2011, 2012, 2013, 2014

2012-10-10

... of new chemicals. In addition under TSCA, EPA is required to publish in the Federal Register a notice of receipt of a premanufacture notice (PMN) or an application for a test marketing exemption (TME... the receipt of notices of commencement (NOC) to manufacture those chemicals. This document, which...

7 CFR 735.401 - Electronic warehouse receipt and USWA electronic document providers.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 7 2013-01-01 2013-01-01 false Electronic warehouse receipt and USWA electronic... UNITED STATES WAREHOUSE ACT Electronic Providers § 735.401 Electronic warehouse receipt and USWA electronic document providers. (a) To establish a USWA-authorized system to issue and transfer EWR's and USWA...

7 CFR 735.401 - Electronic warehouse receipt and USWA electronic document providers.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 7 2014-01-01 2014-01-01 false Electronic warehouse receipt and USWA electronic... UNITED STATES WAREHOUSE ACT Electronic Providers § 735.401 Electronic warehouse receipt and USWA electronic document providers. (a) To establish a USWA-authorized system to issue and transfer EWR's and USWA...

7 CFR 735.401 - Electronic warehouse receipt and USWA electronic document providers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 7 2010-01-01 2010-01-01 false Electronic warehouse receipt and USWA electronic... UNITED STATES WAREHOUSE ACT Electronic Providers § 735.401 Electronic warehouse receipt and USWA electronic document providers. (a) To establish a USWA-authorized system to issue and transfer EWR's and USWA...

7 CFR 735.401 - Electronic warehouse receipt and USWA electronic document providers.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 7 2012-01-01 2012-01-01 false Electronic warehouse receipt and USWA electronic... UNITED STATES WAREHOUSE ACT Electronic Providers § 735.401 Electronic warehouse receipt and USWA electronic document providers. (a) To establish a USWA-authorized system to issue and transfer EWR's and USWA...

7 CFR 735.401 - Electronic warehouse receipt and USWA electronic document providers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 7 2011-01-01 2011-01-01 false Electronic warehouse receipt and USWA electronic... UNITED STATES WAREHOUSE ACT Electronic Providers § 735.401 Electronic warehouse receipt and USWA electronic document providers. (a) To establish a USWA-authorized system to issue and transfer EWR's and USWA...

19 CFR 162.15 - Receipt for seized property.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 2 2010-04-01 2010-04-01 false Receipt for seized property. 162.15 Section 162.15 Customs Duties U.S. CUSTOMS AND BORDER PROTECTION, DEPARTMENT OF HOMELAND SECURITY; DEPARTMENT OF THE TREASURY (CONTINUED) INSPECTION, SEARCH, AND SEIZURE Search Warrants § 162.15 Receipt for seized property...

48 CFR 915.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 5 2014-10-01 2014-10-01 false Exchanges with industry before receipt of proposals. 915.201 Section 915.201 Federal Acquisition Regulations System DEPARTMENT OF... Proposals and Information 915.201 Exchanges with industry before receipt of proposals. (e) Approval for the...

48 CFR 915.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 5 2012-10-01 2012-10-01 false Exchanges with industry before receipt of proposals. 915.201 Section 915.201 Federal Acquisition Regulations System DEPARTMENT OF... Proposals and Information 915.201 Exchanges with industry before receipt of proposals. (e) Approval for the...

48 CFR 915.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 5 2011-10-01 2011-10-01 false Exchanges with industry before receipt of proposals. 915.201 Section 915.201 Federal Acquisition Regulations System DEPARTMENT OF... Proposals and Information 915.201 Exchanges with industry before receipt of proposals. (e) Approval for the...

48 CFR 15.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Exchanges with industry... Receipt of Proposals and Information 15.201 Exchanges with industry before receipt of proposals. (a... requirements and industry capabilities, thereby allowing potential offerors to judge whether or how they can...

48 CFR 15.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 1 2014-10-01 2014-10-01 false Exchanges with industry... Receipt of Proposals and Information 15.201 Exchanges with industry before receipt of proposals. (a... requirements and industry capabilities, thereby allowing potential offerors to judge whether or how they can...

48 CFR 915.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 5 2013-10-01 2013-10-01 false Exchanges with industry before receipt of proposals. 915.201 Section 915.201 Federal Acquisition Regulations System DEPARTMENT OF... Proposals and Information 915.201 Exchanges with industry before receipt of proposals. (e) Approval for the...

48 CFR 15.201 - Exchanges with industry before receipt of proposals.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 1 2012-10-01 2012-10-01 false Exchanges with industry... Receipt of Proposals and Information 15.201 Exchanges with industry before receipt of proposals. (a... requirements and industry capabilities, thereby allowing potential offerors to judge whether or how they can...

33 CFR 150.110 - What are the notification requirements upon receipt of classification society certifications?

Code of Federal Regulations, 2010 CFR

2010-07-01

... requirements upon receipt of classification society certifications? 150.110 Section 150.110 Navigation and... society certifications? The licensee must notify the Captain of the Port, in writing, upon receipt of a classification society certification, interim class certificate, or single point mooring classification...

33 CFR 150.110 - What are the notification requirements upon receipt of classification society certifications?

Code of Federal Regulations, 2011 CFR

2011-07-01

... requirements upon receipt of classification society certifications? 150.110 Section 150.110 Navigation and... society certifications? The licensee must notify the Captain of the Port, in writing, upon receipt of a classification society certification, interim class certificate, or single point mooring classification...

27 CFR 18.56 - Receipt of concentrate.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2013-04-01 2013-04-01 false Receipt of concentrate. 18.56 Section 18.56 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL PRODUCTION OF VOLATILE FRUIT-FLAVOR CONCENTRATE Operations § 18.56 Receipt...

27 CFR 18.56 - Receipt of concentrate.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2014-04-01 2014-04-01 false Receipt of concentrate. 18.56 Section 18.56 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY ALCOHOL PRODUCTION OF VOLATILE FRUIT-FLAVOR CONCENTRATE Operations § 18.56 Receipt...

27 CFR 18.56 - Receipt of concentrate.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2012-04-01 2012-04-01 false Receipt of concentrate. 18.56 Section 18.56 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU, DEPARTMENT OF THE TREASURY LIQUORS PRODUCTION OF VOLATILE FRUIT-FLAVOR CONCENTRATE Operations § 18.56 Receipt...

Tobacco industry direct mail receipt and coupon use among young adult smokers.

PubMed

Jane Lewis, M; Bover Manderski, Michelle T; Delnevo, Cristine D

2015-02-01

To examine young adult smokers' receipt of tobacco industry direct mail and use of coupons to purchase cigarettes. A total of 699 young adults from a 2011 national survey who reported smoking every day/some days provided self-report data on past-six month receipt of direct mail and past-six month use of coupons to purchase cigarettes. Multivariable logistic regression models were used to calculate adjusted odds of direct mail receipt and coupon use. Overall, 25.1% of young adult smokers reported receiving direct mail from a tobacco company and 24.2% had used a coupon to buy cigarettes in the past 6 months. Direct mail receipt and coupon use to purchase cigarettes were significantly higher among females, daily smokers, and whites. Nearly 70% of smokers who received direct mail had also used a coupon to purchase cigarettes in the preceding 6 months. Brand websites were the most commonly reported means of joining a direct mailing list. This study adds to limited research showing receipt of direct mail and use of price reducing coupons by young adults. Also, higher rates of direct mail receipt and coupon use among females suggest that these strategies may be especially effective in encouraging smoking in females. Copyright © 2014 Elsevier Inc. All rights reserved.

Community annotation experiment for ground truth generation for the i2b2 medication challenge

PubMed Central

Solti, Imre; Xia, Fei; Cadag, Eithon

2010-01-01

Objective Within the context of the Third i2b2 Workshop on Natural Language Processing Challenges for Clinical Records, the authors (also referred to as ‘the i2b2 medication challenge team’ or ‘the i2b2 team’ for short) organized a community annotation experiment. Design For this experiment, the authors released annotation guidelines and a small set of annotated discharge summaries. They asked the participants of the Third i2b2 Workshop to annotate 10 discharge summaries per person; each discharge summary was annotated by two annotators from two different teams, and a third annotator from a third team resolved disagreements. Measurements In order to evaluate the reliability of the annotations thus produced, the authors measured community inter-annotator agreement and compared it with the inter-annotator agreement of expert annotators when both the community and the expert annotators generated ground truth based on pooled system outputs. For this purpose, the pool consisted of the three most densely populated automatic annotations of each record. The authors also compared the community inter-annotator agreement with expert inter-annotator agreement when the experts annotated raw records without using the pool. Finally, they measured the quality of the community ground truth by comparing it with the expert ground truth. Results and conclusions The authors found that the community annotators achieved comparable inter-annotator agreement to expert annotators, regardless of whether the experts annotated from the pool. Furthermore, the ground truth generated by the community obtained F-measures above 0.90 against the ground truth of the experts, indicating the value of the community as a source of high-quality ground truth even on intricate and domain-specific annotation tasks. PMID:20819855

Marky: a tool supporting annotation consistency in multi-user and iterative document annotation projects.

PubMed

Pérez-Pérez, Martín; Glez-Peña, Daniel; Fdez-Riverola, Florentino; Lourenço, Anália

2015-02-01

Document annotation is a key task in the development of Text Mining methods and applications. High quality annotated corpora are invaluable, but their preparation requires a considerable amount of resources and time. Although the existing annotation tools offer good user interaction interfaces to domain experts, project management and quality control abilities are still limited. Therefore, the current work introduces Marky, a new Web-based document annotation tool equipped to manage multi-user and iterative projects, and to evaluate annotation quality throughout the project life cycle. At the core, Marky is a Web application based on the open source CakePHP framework. User interface relies on HTML5 and CSS3 technologies. Rangy library assists in browser-independent implementation of common DOM range and selection tasks, and Ajax and JQuery technologies are used to enhance user-system interaction. Marky grants solid management of inter- and intra-annotator work. Most notably, its annotation tracking system supports systematic and on-demand agreement analysis and annotation amendment. Each annotator may work over documents as usual, but all the annotations made are saved by the tracking system and may be further compared. So, the project administrator is able to evaluate annotation consistency among annotators and across rounds of annotation, while annotators are able to reject or amend subsets of annotations made in previous rounds. As a side effect, the tracking system minimises resource and time consumption. Marky is a novel environment for managing multi-user and iterative document annotation projects. Compared to other tools, Marky offers a similar visually intuitive annotation experience while providing unique means to minimise annotation effort and enforce annotation quality, and therefore corpus consistency. Marky is freely available for non-commercial use at http://sing.ei.uvigo.es/marky. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Is the Juice Worth the Squeeze? Costs and Benefits of Multiple Human Annotators for Clinical Text De-identification.

PubMed

Carrell, David S; Cronkite, David J; Malin, Bradley A; Aberdeen, John S; Hirschman, Lynette

2016-08-05

Clinical text contains valuable information but must be de-identified before it can be used for secondary purposes. Accurate annotation of personally identifiable information (PII) is essential to the development of automated de-identification systems and to manual redaction of PII. Yet the accuracy of annotations may vary considerably across individual annotators and annotation is costly. As such, the marginal benefit of incorporating additional annotators has not been well characterized. This study models the costs and benefits of incorporating increasing numbers of independent human annotators to identify the instances of PII in a corpus. We used a corpus with gold standard annotations to evaluate the performance of teams of annotators of increasing size. Four annotators independently identified PII in a 100-document corpus consisting of randomly selected clinical notes from Family Practice clinics in a large integrated health care system. These annotations were pooled and validated to generate a gold standard corpus for evaluation. Recall rates for all PII types ranged from 0.90 to 0.98 for individual annotators to 0.998 to 1.0 for teams of three, when meas-ured against the gold standard. Median cost per PII instance discovered during corpus annotation ranged from $ 0.71 for an individual annotator to $ 377 for annotations discovered only by a fourth annotator. Incorporating a second annotator into a PII annotation process reduces unredacted PII and improves the quality of annotations to 0.99 recall, yielding clear benefit at reasonable cost; the cost advantages of annotation teams larger than two diminish rapidly.

Active learning reduces annotation time for clinical concept extraction.

PubMed

Kholghi, Mahnoosh; Sitbon, Laurianne; Zuccon, Guido; Nguyen, Anthony

2017-10-01

To investigate: (1) the annotation time savings by various active learning query strategies compared to supervised learning and a random sampling baseline, and (2) the benefits of active learning-assisted pre-annotations in accelerating the manual annotation process compared to de novo annotation. There are 73 and 120 discharge summary reports provided by Beth Israel institute in the train and test sets of the concept extraction task in the i2b2/VA 2010 challenge, respectively. The 73 reports were used in user study experiments for manual annotation. First, all sequences within the 73 reports were manually annotated from scratch. Next, active learning models were built to generate pre-annotations for the sequences selected by a query strategy. The annotation/reviewing time per sequence was recorded. The 120 test reports were used to measure the effectiveness of the active learning models. When annotating from scratch, active learning reduced the annotation time up to 35% and 28% compared to a fully supervised approach and a random sampling baseline, respectively. Reviewing active learning-assisted pre-annotations resulted in 20% further reduction of the annotation time when compared to de novo annotation. The number of concepts that require manual annotation is a good indicator of the annotation time for various active learning approaches as demonstrated by high correlation between time rate and concept annotation rate. Active learning has a key role in reducing the time required to manually annotate domain concepts from clinical free text, either when annotating from scratch or reviewing active learning-assisted pre-annotations. Copyright © 2017 Elsevier B.V. All rights reserved.

Corpus annotation for mining biomedical events from literature

PubMed Central

Kim, Jin-Dong; Ohta, Tomoko; Tsujii, Jun'ichi

2008-01-01

Background Advanced Text Mining (TM) such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation. Results We have completed a new type of semantic annotation, event annotation, which is an addition to the existing annotations in the GENIA corpus. The corpus has already been annotated with POS (Parts of Speech), syntactic trees, terms, etc. The new annotation was made on half of the GENIA corpus, consisting of 1,000 Medline abstracts. It contains 9,372 sentences in which 36,114 events are identified. The major challenges during event annotation were (1) to design a scheme of annotation which meets specific requirements of text annotation, (2) to achieve biology-oriented annotation which reflect biologists' interpretation of text, and (3) to ensure the homogeneity of annotation quality across annotators. To meet these challenges, we introduced new concepts such as Single-facet Annotation and Semantic Typing, which have collectively contributed to successful completion of a large scale annotation. Conclusion The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing)-based TM in the bio-medical domain. PMID:18182099

46 CFR 560.5 - Receipt of relevant information.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 9 2010-10-01 2010-10-01 false Receipt of relevant information. 560.5 Section 560.5... FOREIGN PORTS § 560.5 Receipt of relevant information. (a) In making its decision on matters arising under... submissions should be supported by affidavits of fact and memorandum of law. Relevant information may include...

21 CFR 203.60 - Request and receipt forms, reports, and records.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 4 2010-04-01 2010-04-01 false Request and receipt forms, reports, and records. 203.60 Section 203.60 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) DRUGS: GENERAL PRESCRIPTION DRUG MARKETING Request and Receipt Forms, Reports, and...

27 CFR 17.165 - Receipt of raw ingredients.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2011-04-01 2011-04-01 false Receipt of raw ingredients. 17.165 Section 17.165 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU... PRODUCTS Records § 17.165 Receipt of raw ingredients. For raw ingredients destined to be used in...

27 CFR 17.165 - Receipt of raw ingredients.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Receipt of raw ingredients. 17.165 Section 17.165 Alcohol, Tobacco Products and Firearms ALCOHOL AND TOBACCO TAX AND TRADE BUREAU... PRODUCTS Records § 17.165 Receipt of raw ingredients. For raw ingredients destined to be used in...

34 CFR 668.122 - Determination of filing, receipt, and submission dates.

Code of Federal Regulations, 2010 CFR

2010-07-01

..., receipt, and submission dates. (a) The request for review, appeals, and other written submissions referred to in this subpart may be either hand-delivered or mailed. (b) All mailed written submissions... of filing, receipt, or submission dates shall be based on either the date of hand-delivery or the...

15 CFR 904.102 - Procedures upon receipt of a NOVA.

Code of Federal Regulations, 2010 CFR

2010-01-01

... (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE GENERAL REGULATIONS CIVIL PROCEDURES Civil Penalties § 904.102 Procedures upon receipt of a NOVA. (a) The respondent has 30 days from... 15 Commerce and Foreign Trade 3 2010-01-01 2010-01-01 false Procedures upon receipt of a NOVA. 904...

15 CFR 904.102 - Procedures upon receipt of a NOVA.

Code of Federal Regulations, 2011 CFR

2011-01-01

... (Continued) NATIONAL OCEANIC AND ATMOSPHERIC ADMINISTRATION, DEPARTMENT OF COMMERCE GENERAL REGULATIONS CIVIL PROCEDURES Civil Penalties § 904.102 Procedures upon receipt of a NOVA. (a) The respondent has 30 days from... 15 Commerce and Foreign Trade 3 2011-01-01 2011-01-01 false Procedures upon receipt of a NOVA. 904...

75 FR 39720 - Self-Regulatory Organizations; Notice of Filing and Immediate Effectiveness of Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-12

..., Inc. To List Options on Trust Issued Receipts in $1 Strike Intervals July 6, 2010. Pursuant to Section... strike price intervals for options on Trust Issued Receipts. The text of the proposed rule change is... strike price intervals for options on Trust Issued Receipts (``TIRs''), including Holding Company...

75 FR 42471 - Self-Regulatory Organizations; NYSE Arca, Inc.; Order Granting Accelerated Approval of Proposed...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-21

... Commission (``Commission''), pursuant to Section 19(b)(1) of the Securities Exchange Act of 1934 (``Act'') \\1... addition includes other Depositary Receipts (``DRs''), which include Global Depositary Receipts (``GDRs''), Euro Depositary Receipts (``Euro DRs'') and New York Shares (``NYSs'').\\6\\ \\4\\ The Trust is registered...

26 CFR 1.199-3 - Domestic production gross receipts.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 3 2010-04-01 2010-04-01 false Domestic production gross receipts. 1.199-3 Section 1.199-3 Internal Revenue INTERNAL REVENUE SERVICE, DEPARTMENT OF THE TREASURY (CONTINUED) INCOME TAX (CONTINUED) INCOME TAXES Itemized Deductions for Individuals and Corporations (continued) § 1.199-3 Domestic production gross receipts. (a) In...

Neighborhood Social Influence and Welfare Receipt in Sweden: A Panel Data Analysis

ERIC Educational Resources Information Center

Mood, Carina

2010-01-01

This article places the choice to claim welfare benefits in a social context by studying how neighborhood welfare receipt affects welfare receipt among couples in Stockholm, Sweden. It is expected that the propensity to claim welfare should increase with welfare use in the neighborhood, primarily through stigma reduction and increasing…

77 FR 39442 - Receipts-Based, Small Business Size Standard

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-03

... RIN 3150-AJ14 [NRC-2012-0062] Receipts-Based, Small Business Size Standard AGENCY: Nuclear Regulatory... business size standard from $6.5 million to $7 million to conform to the standard set by the Small Business... updating the receipts-based, small business size standard from $6.5 million to $7.0 million. Adequate...

28 CFR 8.4 - Custody of seized property, inventory and receipt.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 28 Judicial Administration 1 2011-07-01 2011-07-01 false Custody of seized property, inventory and receipt. 8.4 Section 8.4 Judicial Administration DEPARTMENT OF JUSTICE FBI FORFEITURE AUTHORITY FOR CERTAIN STATUTES § 8.4 Custody of seized property, inventory and receipt. All property seized pursuant to...

28 CFR 8.4 - Custody of seized property, inventory and receipt.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Custody of seized property, inventory and receipt. 8.4 Section 8.4 Judicial Administration DEPARTMENT OF JUSTICE FBI FORFEITURE AUTHORITY FOR CERTAIN STATUTES § 8.4 Custody of seized property, inventory and receipt. All property seized pursuant to...

28 CFR 8.4 - Custody of seized property, inventory and receipt.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 28 Judicial Administration 1 2012-07-01 2012-07-01 false Custody of seized property, inventory and receipt. 8.4 Section 8.4 Judicial Administration DEPARTMENT OF JUSTICE FBI FORFEITURE AUTHORITY FOR CERTAIN STATUTES § 8.4 Custody of seized property, inventory and receipt. All property seized pursuant to...

78 FR 66700 - Toxic Substances Control Act Chemical Testing; Receipt of Test Data

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-06

... Chemical Testing; Receipt of Test Data AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: This notice announces EPA's receipt of test data on 21 chemicals. These data were submitted pursuant to 3 test rules issued by EPA under section 4 of the Toxic Substance Control Act (TSCA). The...

78 FR 69414 - Toxic Substances Control Act Chemical Testing; Receipt of Test Data

Federal Register 2010, 2011, 2012, 2013, 2014

2013-11-19

... Chemical Testing; Receipt of Test Data AGENCY: Environmental Protection Agency (EPA). ACTION: Notice. SUMMARY: This notice announces EPA's receipt of test data on 1- propanesulfonic acid, 2-hydroxy-3-(2-propen-1-yloxy)-, sodium salt (1:1). These data were submitted pursuant to a test rule issued by EPA...

76 FR 64966 - Notice of Availability of a Draft Environmental Assessment and Receipt of an Application for an...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-10-19

...] Notice of Availability of a Draft Environmental Assessment and Receipt of an Application for an... Wildlife Service, Interior. ACTION: Notice of availability of draft environmental assessment, receipt of... Grid (NG), Syracuse, New York, and draft environmental assessment (EA) for public review and comment...

19 CFR 24.3 - Bills and accounts; receipts.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 19 Customs Duties 1 2010-04-01 2010-04-01 false Bills and accounts; receipts. 24.3 Section 24.3... TREASURY CUSTOMS FINANCIAL AND ACCOUNTING PROCEDURE § 24.3 Bills and accounts; receipts. (a) Any bill or... document filed by the payer and the payer's cancelled check shall constitute evidence of payment. (c) A...

19 CFR 24.3 - Bills and accounts; receipts.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 19 Customs Duties 1 2012-04-01 2012-04-01 false Bills and accounts; receipts. 24.3 Section 24.3... TREASURY CUSTOMS FINANCIAL AND ACCOUNTING PROCEDURE § 24.3 Bills and accounts; receipts. (a) Any bill or... document filed by the payer and the payer's cancelled check shall constitute evidence of payment. (c) A...

19 CFR 24.3 - Bills and accounts; receipts.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 19 Customs Duties 1 2013-04-01 2013-04-01 false Bills and accounts; receipts. 24.3 Section 24.3... TREASURY CUSTOMS FINANCIAL AND ACCOUNTING PROCEDURE § 24.3 Bills and accounts; receipts. (a) Any bill or... document filed by the payer and the payer's cancelled check shall constitute evidence of payment. (c) A...

19 CFR 24.3 - Bills and accounts; receipts.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 19 Customs Duties 1 2014-04-01 2014-04-01 false Bills and accounts; receipts. 24.3 Section 24.3... TREASURY CUSTOMS FINANCIAL AND ACCOUNTING PROCEDURE § 24.3 Bills and accounts; receipts. (a) Any bill or... document filed by the payer and the payer's cancelled check shall constitute evidence of payment. (c) A...

19 CFR 24.3 - Bills and accounts; receipts.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 19 Customs Duties 1 2011-04-01 2011-04-01 false Bills and accounts; receipts. 24.3 Section 24.3... TREASURY CUSTOMS FINANCIAL AND ACCOUNTING PROCEDURE § 24.3 Bills and accounts; receipts. (a) Any bill or... document filed by the payer and the payer's cancelled check shall constitute evidence of payment. (c) A...

75 FR 4103 - Receipt of Applications for Permit

Federal Register 2010, 2011, 2012, 2013, 2014

2010-01-26

... DEPARTMENT OF THE INTERIOR Fish and Wildlife Service [FWS-R9-IA-2009-N011] [96300-1671-0000-P5] Receipt of Applications for Permit AGENCY: Fish and Wildlife Service, Interior. ACTION: Notice of receipt of applications for permit. SUMMARY: We, the U.S. Fish and Wildlife Service, invite the public to...

Protein structure based prediction of catalytic residues.

PubMed

Fajardo, J Eduardo; Fiser, Andras

2013-02-22

Worldwide structural genomics projects continue to release new protein structures at an unprecedented pace, so far nearly 6000, but only about 60% of these proteins have any sort of functional annotation. We explored a range of features that can be used for the prediction of functional residues given a known three-dimensional structure. These features include various centrality measures of nodes in graphs of interacting residues: closeness, betweenness and page-rank centrality. We also analyzed the distance of functional amino acids to the general center of mass (GCM) of the structure, relative solvent accessibility (RSA), and the use of relative entropy as a measure of sequence conservation. From the selected features, neural networks were trained to identify catalytic residues. We found that using distance to the GCM together with amino acid type provide a good discriminant function, when combined independently with sequence conservation. Using an independent test set of 29 annotated protein structures, the method returned 411 of the initial 9262 residues as the most likely to be involved in function. The output 411 residues contain 70 of the annotated 111 catalytic residues. This represents an approximately 14-fold enrichment of catalytic residues on the entire input set (corresponding to a sensitivity of 63% and a precision of 17%), a performance competitive with that of other state-of-the-art methods. We found that several of the graph based measures utilize the same underlying feature of protein structures, which can be simply and more effectively captured with the distance to GCM definition. This also has the added the advantage of simplicity and easy implementation. Meanwhile sequence conservation remains by far the most influential feature in identifying functional residues. We also found that due the rapid changes in size and composition of sequence databases, conservation calculations must be recalibrated for specific reference databases.

High-coverage sequencing and annotated assembly of the genome of the Australian dragon lizard Pogona vitticeps.

PubMed

Georges, Arthur; Li, Qiye; Lian, Jinmin; O'Meally, Denis; Deakin, Janine; Wang, Zongji; Zhang, Pei; Fujita, Matthew; Patel, Hardip R; Holleley, Clare E; Zhou, Yang; Zhang, Xiuwen; Matsubara, Kazumi; Waters, Paul; Graves, Jennifer A Marshall; Sarre, Stephen D; Zhang, Guojie

2015-01-01

The lizards of the family Agamidae are one of the most prominent elements of the Australian reptile fauna. Here, we present a genomic resource built on the basis of a wild-caught male ZZ central bearded dragon Pogona vitticeps. The genomic sequence for P. vitticeps, generated on the Illumina HiSeq 2000 platform, comprised 317 Gbp (179X raw read depth) from 13 insert libraries ranging from 250 bp to 40 kbp. After filtering for low-quality and duplicated reads, 146 Gbp of data (83X) was available for assembly. Exceptionally high levels of heterozygosity (0.85 % of single nucleotide polymorphisms plus sequence insertions or deletions) complicated assembly; nevertheless, 96.4 % of reads mapped back to the assembled scaffolds, indicating that the assembly included most of the sequenced genome. Length of the assembly was 1.8 Gbp in 545,310 scaffolds (69,852 longer than 300 bp), the longest being 14.68 Mbp. N50 was 2.29 Mbp. Genes were annotated on the basis of de novo prediction, similarity to the green anole Anolis carolinensis, Gallus gallus and Homo sapiens proteins, and P. vitticeps transcriptome sequence assemblies, to yield 19,406 protein-coding genes in the assembly, 63 % of which had intact open reading frames. Our assembly captured 99 % (246 of 248) of core CEGMA genes, with 93 % (231) being complete. The quality of the P. vitticeps assembly is comparable or superior to that of other published squamate genomes, and the annotated P. vitticeps genome can be accessed through a genome browser available at https://genomics.canberra.edu.au.

Challenges for automatically extracting molecular interactions from full-text articles.

PubMed

McIntosh, Tara; Curran, James R

2009-09-24

The increasing availability of full-text biomedical articles will allow more biomedical knowledge to be extracted automatically with greater reliability. However, most Information Retrieval (IR) and Extraction (IE) tools currently process only abstracts. The lack of corpora has limited the development of tools that are capable of exploiting the knowledge in full-text articles. As a result, there has been little investigation into the advantages of full-text document structure, and the challenges developers will face in processing full-text articles. We manually annotated passages from full-text articles that describe interactions summarised in a Molecular Interaction Map (MIM). Our corpus tracks the process of identifying facts to form the MIM summaries and captures any factual dependencies that must be resolved to extract the fact completely. For example, a fact in the results section may require a synonym defined in the introduction. The passages are also annotated with negated and coreference expressions that must be resolved.We describe the guidelines for identifying relevant passages and possible dependencies. The corpus includes 2162 sentences from 78 full-text articles. Our corpus analysis demonstrates the necessity of full-text processing; identifies the article sections where interactions are most commonly stated; and quantifies the proportion of interaction statements requiring coherent dependencies. Further, it allows us to report on the relative importance of identifying synonyms and resolving negated expressions. We also experiment with an oracle sentence retrieval system using the corpus as a gold-standard evaluation set. We introduce the MIM corpus, a unique resource that maps interaction facts in a MIM to annotated passages within full-text articles. It is an invaluable case study providing guidance to developers of biomedical IR and IE systems, and can be used as a gold-standard evaluation set for full-text IR tasks.

Annotating Diseases Using Human Phenotype Ontology Improves Prediction of Disease-Associated Long Non-coding RNAs.

PubMed

Le, Duc-Hau; Dao, Lan T M

2018-05-23

Recently, many long non-coding RNAs (lncRNAs) have been identified and their biological function has been characterized; however, our understanding of their underlying molecular mechanisms related to disease is still limited. To overcome the limitation in experimentally identifying disease-lncRNA associations, computational methods have been proposed as a powerful tool to predict such associations. These methods are usually based on the similarities between diseases or lncRNAs since it was reported that similar diseases are associated with functionally similar lncRNAs. Therefore, prediction performance is highly dependent on how well the similarities can be captured. Previous studies have calculated the similarity between two diseases by mapping exactly each disease to a single Disease Ontology (DO) term, and then use a semantic similarity measure to calculate the similarity between them. However, the problem of this approach is that a disease can be described by more than one DO terms. Until now, there is no annotation database of DO terms for diseases except for genes. In contrast, Human Phenotype Ontology (HPO) is designed to fully annotate human disease phenotypes. Therefore, in this study, we constructed disease similarity networks/matrices using HPO instead of DO. Then, we used these networks/matrices as inputs of two representative machine learning-based and network-based ranking algorithms, that is, regularized least square and heterogeneous graph-based inference, respectively. The results showed that the prediction performance of the two algorithms on HPO-based is better than that on DO-based networks/matrices. In addition, our method can predict 11 novel cancer-associated lncRNAs, which are supported by literature evidence. Copyright © 2018 Elsevier Ltd. All rights reserved.

CNV Workshop: an integrated platform for high-throughput copy number variation discovery and clinical diagnostics.

PubMed

Gai, Xiaowu; Perin, Juan C; Murphy, Kevin; O'Hara, Ryan; D'arcy, Monica; Wenocur, Adam; Xie, Hongbo M; Rappaport, Eric F; Shaikh, Tamim H; White, Peter S

2010-02-04

Recent studies have shown that copy number variations (CNVs) are frequent in higher eukaryotes and associated with a substantial portion of inherited and acquired risk for various human diseases. The increasing availability of high-resolution genome surveillance platforms provides opportunity for rapidly assessing research and clinical samples for CNV content, as well as for determining the potential pathogenicity of identified variants. However, few informatics tools for accurate and efficient CNV detection and assessment currently exist. We developed a suite of software tools and resources (CNV Workshop) for automated, genome-wide CNV detection from a variety of SNP array platforms. CNV Workshop includes three major components: detection, annotation, and presentation of structural variants from genome array data. CNV detection utilizes a robust and genotype-specific extension of the Circular Binary Segmentation algorithm, and the use of additional detection algorithms is supported. Predicted CNVs are captured in a MySQL database that supports cohort-based projects and incorporates a secure user authentication layer and user/admin roles. To assist with determination of pathogenicity, detected CNVs are also annotated automatically for gene content, known disease loci, and gene-based literature references. Results are easily queried, sorted, filtered, and visualized via a web-based presentation layer that includes a GBrowse-based graphical representation of CNV content and relevant public data, integration with the UCSC Genome Browser, and tabular displays of genomic attributes for each CNV. To our knowledge, CNV Workshop represents the first cohesive and convenient platform for detection, annotation, and assessment of the biological and clinical significance of structural variants. CNV Workshop has been successfully utilized for assessment of genomic variation in healthy individuals and disease cohorts and is an ideal platform for coordinating multiple associated projects. Available on the web at: http://sourceforge.net/projects/cnv.

Racial and ethnic disparities in the receipt of cancer treatment.

PubMed

Shavers, Vickie L; Brown, Martin L

2002-03-06

A disproportionate number of cancer deaths occur among racial/ethnic minorities, particularly African Americans, who have a 33% higher risk of dying of cancer than whites. Although differences in incidence and stage of disease at diagnosis may contribute to racial disparities in mortality, evidence of racial disparities in the receipt of treatment of other chronic diseases raises questions about the possible role of inequities in the receipt of cancer treatment. To evaluate racial/ethnic disparities in the receipt of cancer treatment, we examined the published literature that addressed access/use of specific cancer treatment procedures, trends in patterns of use, or survival studies. We found evidence of racial disparities in receipt of definitive primary therapy, conservative therapy, and adjuvant therapy. These treatment differences could not be completely explained by racial/ethnic variation in clinically relevant factors. In many studies, these treatment differences were associated with an adverse impact on the health outcomes of racial/ethnic minorities, including more frequent recurrence, shorter disease-free survival, and higher mortality. Reducing the influence of nonclinical factors on the receipt of cancer treatment may, therefore, provide an important means of reducing racial/ethnic disparities in health. New data resources and improved study methodology are needed to better identify and quantify the full spectrum of nonclinical factors that contribute to the higher cancer mortality among racial/ethnic minorities and to develop strategies to facilitate receipt of appropriate cancer care for all patients.

The UniProtKB guide to the human proteome

PubMed Central

Breuza, Lionel; Poux, Sylvain; Estreicher, Anne; Famiglietti, Maria Livia; Magrane, Michele; Tognolli, Michael; Bridge, Alan; Baratin, Delphine; Redaschi, Nicole

2016-01-01

Advances in high-throughput and advanced technologies allow researchers to routinely perform whole genome and proteome analysis. For this purpose, they need high-quality resources providing comprehensive gene and protein sets for their organisms of interest. Using the example of the human proteome, we will describe the content of a complete proteome in the UniProt Knowledgebase (UniProtKB). We will show how manual expert curation of UniProtKB/Swiss-Prot is complemented by expert-driven automatic annotation to build a comprehensive, high-quality and traceable resource. We will also illustrate how the complexity of the human proteome is captured and structured in UniProtKB. Database URL: www.uniprot.org PMID:26896845

Geologic Map of the Utukok River Quadrangle, Alaska

USGS Publications Warehouse

Mull, Charles G.; Houseknecht, David W.; Pessel, G.H.; Garrity, Christopher P.

2006-01-01

This map is a product of the USGS Digital Geologic Maps of Northern Alaska project, which captures in digital format quadrangles across the entire width of northern Alaska. Sources include geologic maps previously published in hardcopy format and recent updates and revisions based on field mapping by the Alaska Department of Natural Resources, Division of Geological and Geophysical Surveys and Division of Oil and Gas, and the U.S. Geological Survey. Individual quadrangles are digitized at either 1:125,000 or 1:250,000 depending on the resolution of source maps. The project objective is to produce a set of digital geologic maps with uniform stratigraphic nomenclature and structural annotation, and publish those maps electronically.

Overview of the gene ontology task at BioCreative IV.

PubMed

Mao, Yuqing; Van Auken, Kimberly; Li, Donghui; Arighi, Cecilia N; McQuilton, Peter; Hayman, G Thomas; Tweedie, Susan; Schaeffer, Mary L; Laulederkind, Stanley J F; Wang, Shur-Jen; Gobeill, Julien; Ruch, Patrick; Luu, Anh Tuan; Kim, Jung-Jae; Chiang, Jung-Hsien; Chen, Yu-De; Yang, Chia-Jung; Liu, Hongfang; Zhu, Dongqing; Li, Yanpeng; Yu, Hong; Emadzadeh, Ehsan; Gonzalez, Graciela; Chen, Jian-Ming; Dai, Hong-Jie; Lu, Zhiyong

2014-01-01

Gene ontology (GO) annotation is a common task among model organism databases (MODs) for capturing gene function data from journal articles. It is a time-consuming and labor-intensive task, and is thus often considered as one of the bottlenecks in literature curation. There is a growing need for semiautomated or fully automated GO curation techniques that will help database curators to rapidly and accurately identify gene function information in full-length articles. Despite multiple attempts in the past, few studies have proven to be useful with regard to assisting real-world GO curation. The shortage of sentence-level training data and opportunities for interaction between text-mining developers and GO curators has limited the advances in algorithm development and corresponding use in practical circumstances. To this end, we organized a text-mining challenge task for literature-based GO annotation in BioCreative IV. More specifically, we developed two subtasks: (i) to automatically locate text passages that contain GO-relevant information (a text retrieval task) and (ii) to automatically identify relevant GO terms for the genes in a given article (a concept-recognition task). With the support from five MODs, we provided teams with >4000 unique text passages that served as the basis for each GO annotation in our task data. Such evidence text information has long been recognized as critical for text-mining algorithm development but was never made available because of the high cost of curation. In total, seven teams participated in the challenge task. From the team results, we conclude that the state of the art in automatically mining GO terms from literature has improved over the past decade while much progress is still needed for computer-assisted GO curation. Future work should focus on addressing remaining technical challenges for improved performance of automatic GO concept recognition and incorporating practical benefits of text-mining tools into real-world GO annotation. http://www.biocreative.org/tasks/biocreative-iv/track-4-GO/. Published by Oxford University Press 2014. This work is written by US Government employees and is in the public domain in the US.

77 FR 67732 - Notice of Receipt of Petition for Decision That Nonconforming 2009 Porsche Cayenne S Multipurpose...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-13

... the word ``brake'' on the brake failure indicator lamp in place of the international ECE warning...: Installation of U.S.-model software to ensure that the power- operated window system meets the requirements of... Administration, DOT. ACTION: Notice of receipt of petition. SUMMARY: This document announces receipt by the...

31 CFR 245.8 - Receipt or recovery of original check.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 31 Money and Finance: Treasury 2 2010-07-01 2010-07-01 false Receipt or recovery of original check... CHECKS § 245.8 Receipt or recovery of original check. (a) If the original check is received or recovered... of instructions with respect to the negotiability of such check. (b) If the original check is...

27 CFR 19.372 - Receipt of spirits, wines and alcoholic flavoring materials for processing.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 27 Alcohol, Tobacco Products and Firearms 1 2010-04-01 2010-04-01 false Receipt of spirits, wines... Spirits, Wines and Alcoholic Flavoring Materials § 19.372 Receipt of spirits, wines and alcoholic...) Wines (i) from the storage account at the same plant, or (ii) by transfer in bond from a bonded wine...

5 CFR 846.726 - Delegation of authority to act as OPM's agent for receipt of employee communications relating to...

Code of Federal Regulations, 2010 CFR

2010-01-01

....726 Delegation of authority to act as OPM's agent for receipt of employee communications relating to... 5 Administrative Personnel 2 2010-01-01 2010-01-01 false Delegation of authority to act as OPM's agent for receipt of employee communications relating to elections. 846.726 Section 846.726...

48 CFR 29.401-4 - New Mexico gross receipts and compensating tax.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 1 2010-10-01 2010-10-01 false New Mexico gross receipts... ACQUISITION REGULATION GENERAL CONTRACTING REQUIREMENTS TAXES Contract Clauses 29.401-4 New Mexico gross... Gross Receipts and Compensating Tax Act of the State of New Mexico, Sec. 7-9-3(k) NM SA 1978, and means...

39 CFR 2.2 - Agent for receipt of process.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 39 Postal Service 1 2013-07-01 2013-07-01 false Agent for receipt of process. 2.2 Section 2.2 Postal Service UNITED STATES POSTAL SERVICE THE BOARD OF GOVERNORS OF THE U.S. POSTAL SERVICE GENERAL AND TECHNICAL PROVISIONS (ARTICLE II) § 2.2 Agent for receipt of process. The General Counsel of the Postal...

39 CFR 2.2 - Agent for receipt of process.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 39 Postal Service 1 2012-07-01 2012-07-01 false Agent for receipt of process. 2.2 Section 2.2 Postal Service UNITED STATES POSTAL SERVICE THE BOARD OF GOVERNORS OF THE U.S. POSTAL SERVICE GENERAL AND TECHNICAL PROVISIONS (ARTICLE II) § 2.2 Agent for receipt of process. The General Counsel of the Postal...

39 CFR 2.2 - Agent for receipt of process.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 39 Postal Service 1 2014-07-01 2014-07-01 false Agent for receipt of process. 2.2 Section 2.2 Postal Service UNITED STATES POSTAL SERVICE THE BOARD OF GOVERNORS OF THE U.S. POSTAL SERVICE GENERAL AND TECHNICAL PROVISIONS (ARTICLE II) § 2.2 Agent for receipt of process. The General Counsel of the Postal...

39 CFR 2.2 - Agent for receipt of process.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 39 Postal Service 1 2010-07-01 2010-07-01 false Agent for receipt of process. 2.2 Section 2.2 Postal Service UNITED STATES POSTAL SERVICE THE BOARD OF GOVERNORS OF THE U.S. POSTAL SERVICE GENERAL AND TECHNICAL PROVISIONS (ARTICLE II) § 2.2 Agent for receipt of process. The General Counsel of the Postal...

39 CFR 2.2 - Agent for receipt of process.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 39 Postal Service 1 2011-07-01 2011-07-01 false Agent for receipt of process. 2.2 Section 2.2 Postal Service UNITED STATES POSTAL SERVICE THE BOARD OF GOVERNORS OF THE U.S. POSTAL SERVICE GENERAL AND TECHNICAL PROVISIONS (ARTICLE II) § 2.2 Agent for receipt of process. The General Counsel of the Postal...

Veneer-log production and receipts, North Central Region, 1974.

Treesearch

James E. Blyth; Jerold T. Hahn

1976-01-01

Shows 1974 veneer-log production and receipts by species in the Lake States (Michigan, Minnesota, and Wisconsin) and in the Central States (Illinois, Indiana, Iowa, and Missouri). Comparisons are made with similar data for 1972. Includes tables showing veneer-log production and receipts (for selected years) since 1946 in the Lake States and since 1956 in the Central...

Veneer-log production and receipts, North Central Region, 1976.

Treesearch

James E. Blyth; Jerold T. Hahn

1978-01-01

Shows 1976 veneer-log production and receipts by species in the Lake States (Michigan, Minnesota, and Wisconsin) and in the Central States (Illinois, Indiana, Iowa, and Missouri). Comparisons are made with similar data for 1974. Includes tables showing veneer-log production and receipts (for selected years) since 1946 in the Lake States and since 1956 in the Central...

36 CFR 1120.31 - A&TBCB receipt of requests; responsibilities of Freedom of Information Officer.

Code of Federal Regulations, 2010 CFR

2010-07-01

...; responsibilities of Freedom of Information Officer. 1120.31 Section 1120.31 Parks, Forests, and Public Property... Available Upon Request § 1120.31 A&TBCB receipt of requests; responsibilities of Freedom of Information Officer. (a) Upon receipt of a written request, the Freedom of Information Officer must mark the request...

Spatial Allocation of Timber Product Output Roundwood Receipts

Treesearch

John P. Brown

2015-01-01

Data from Georgia timber product output studies were used to develop models that spatially allocate roundwood receipts data from primary wood-using mills. Mill receipts data were converted to a cumulative frequency based on a distance from the mill to a county center. Distances were calculated as either straight line or shortest road distance, and county centers were...

Commission versus Receipt of Violence during Pregnancy: Associations with Substance Abuse Variables

ERIC Educational Resources Information Center

Tzilos, Golfo K.; Grekin, Emily R.; Beatty, Jessica R.; Chase, Sara K.; Ondersma, Steven J.

2010-01-01

The tendency for women to report both commission and receipt of violence is an understudied phenomenon. In particular, little is known about individual differences as a function of commission vs. receipt of partner violence among pregnant women. Using a sample of 78 cohabiting low-SES pregnant women, the current study examines three violence…

75 FR 40011 - Self-Regulatory Organizations; Notice of Filing and Immediate Effectiveness of Proposed Rule...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-13

... LLC To List Options on Trust Issued Receipts in $1 Strike Intervals July 6, 2010. Pursuant to section... strike price intervals for options on Trust Issued Receipts. The text of the proposed rule change is... establish strike price intervals for options on Trust Issued Receipts (``TIRs''), including Holding Company...

48 CFR 29.401-4 - New Mexico gross receipts and compensating tax.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 1 2012-10-01 2012-10-01 false New Mexico gross receipts... ACQUISITION REGULATION GENERAL CONTRACTING REQUIREMENTS TAXES Contract Clauses 29.401-4 New Mexico gross... Gross Receipts and Compensating Tax Act of the State of New Mexico, Sec. 7-9-3(k) NM SA 1978, and means...

48 CFR 29.401-4 - New Mexico gross receipts and compensating tax.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false New Mexico gross receipts... ACQUISITION REGULATION GENERAL CONTRACTING REQUIREMENTS TAXES Contract Clauses 29.401-4 New Mexico gross... Gross Receipts and Compensating Tax Act of the State of New Mexico, Sec. 7-9-3(k) NM SA 1978, and means...

48 CFR 29.401-4 - New Mexico gross receipts and compensating tax.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 1 2014-10-01 2014-10-01 false New Mexico gross receipts... ACQUISITION REGULATION GENERAL CONTRACTING REQUIREMENTS TAXES Contract Clauses 29.401-4 New Mexico gross... Gross Receipts and Compensating Tax Act of the State of New Mexico, Sec. 7-9-3(k) NM SA 1978, and means...

48 CFR 29.401-4 - New Mexico gross receipts and compensating tax.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false New Mexico gross receipts... ACQUISITION REGULATION GENERAL CONTRACTING REQUIREMENTS TAXES Contract Clauses 29.401-4 New Mexico gross... Gross Receipts and Compensating Tax Act of the State of New Mexico, Sec. 7-9-3(k) NM SA 1978, and means...

39 CFR 762.41 - Advice of non-receipt or loss, destruction, or mutilation.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 39 Postal Service 1 2011-07-01 2011-07-01 false Advice of non-receipt or loss, destruction, or..., Mutilated, and Defaced Disbursement Postal Money Orders § 762.41 Advice of non-receipt or loss, destruction... purpose for which it was issued, giving, if possible, its date, number, and amount, and requesting that...

39 CFR 762.41 - Advice of non-receipt or loss, destruction, or mutilation.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 39 Postal Service 1 2010-07-01 2010-07-01 false Advice of non-receipt or loss, destruction, or..., Mutilated, and Defaced Disbursement Postal Money Orders § 762.41 Advice of non-receipt or loss, destruction... purpose for which it was issued, giving, if possible, its date, number, and amount, and requesting that...

49 CFR 805.735-5 - Receipt of gifts, entertainment, and favors by Members or employees.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 7 2011-10-01 2011-10-01 false Receipt of gifts, entertainment, and favors by... Receipt of gifts, entertainment, and favors by Members or employees. (a) Except as provided in paragraphs..., any gift, gratuity, favor, entertainment, loan, or any other thing of monetary value, from a person...

8 CFR 245.15 - Adjustment of status of certain Haitian nationals under the Haitian Refugee Immigrant Fairness...

Code of Federal Regulations, 2010 CFR

2010-01-01

..., unless the Director refers the applicant for a personal interview at a local Service office as provided... records; (ii) Rental receipts; (iii) Utility bill receipts; (iv) Any other dated receipts; (v) Personal...) Adjudication of HRIFA applications filed with the Service—(1) Referral for interview. Except as provided in...

8 CFR 1245.15 - Adjustment of status of certain Haitian nationals under the Haitian Refugee Immigrant Fairness...

Code of Federal Regulations, 2010 CFR

2010-01-01

..., unless the Director refers the applicant for a personal interview at a local Service office as provided... records; (ii) Rental receipts; (iii) Utility bill receipts; (iv) Any other dated receipts; (v) Personal...) Adjudication of HRIFA applications filed with the Service—(1) Referral for interview. Except as provided in...

47 CFR 80.1119 - Receipt and acknowledgement of distress alerts by coast stations and coast earth stations.

Code of Federal Regulations, 2013 CFR

2013-10-01

... by coast stations and coast earth stations. 80.1119 Section 80.1119 Telecommunication FEDERAL... § 80.1119 Receipt and acknowledgement of distress alerts by coast stations and coast earth stations. (a... for coast stations.) (b) Coast earth stations in receipt of distress alerts must ensure that they are...

47 CFR 80.1119 - Receipt and acknowledgement of distress alerts by coast stations and coast earth stations.

Code of Federal Regulations, 2010 CFR

2010-10-01

... by coast stations and coast earth stations. 80.1119 Section 80.1119 Telecommunication FEDERAL... § 80.1119 Receipt and acknowledgement of distress alerts by coast stations and coast earth stations. (a... for coast stations.) (b) Coast earth stations in receipt of distress alerts must ensure that they are...

47 CFR 80.1119 - Receipt and acknowledgement of distress alerts by coast stations and coast earth stations.

Code of Federal Regulations, 2012 CFR

2012-10-01

... by coast stations and coast earth stations. 80.1119 Section 80.1119 Telecommunication FEDERAL... § 80.1119 Receipt and acknowledgement of distress alerts by coast stations and coast earth stations. (a... for coast stations.) (b) Coast earth stations in receipt of distress alerts must ensure that they are...

47 CFR 80.1119 - Receipt and acknowledgement of distress alerts by coast stations and coast earth stations.

Code of Federal Regulations, 2011 CFR

2011-10-01

... by coast stations and coast earth stations. 80.1119 Section 80.1119 Telecommunication FEDERAL... § 80.1119 Receipt and acknowledgement of distress alerts by coast stations and coast earth stations. (a... for coast stations.) (b) Coast earth stations in receipt of distress alerts must ensure that they are...

47 CFR 80.1119 - Receipt and acknowledgement of distress alerts by coast stations and coast earth stations.

Code of Federal Regulations, 2014 CFR

2014-10-01

... by coast stations and coast earth stations. 80.1119 Section 80.1119 Telecommunication FEDERAL... § 80.1119 Receipt and acknowledgement of distress alerts by coast stations and coast earth stations. (a... for coast stations.) (b) Coast earth stations in receipt of distress alerts must ensure that they are...

47 CFR 80.1117 - Procedure for receipt and acknowledgement of distress alerts.

Code of Federal Regulations, 2014 CFR

2014-10-01

... radiotelephony of receipt of a distress alert from a ship station or a ship earth station must be given in the... telegraphy of receipt of a distress alert from a ship earth station must be given by the coast earth station... distress alerts. 80.1117 Section 80.1117 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED...

47 CFR 80.1117 - Procedure for receipt and acknowledgement of distress alerts.

Code of Federal Regulations, 2013 CFR

2013-10-01

... radiotelephony of receipt of a distress alert from a ship station or a ship earth station must be given in the... telegraphy of receipt of a distress alert from a ship earth station must be given by the coast earth station... distress alerts. 80.1117 Section 80.1117 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED...

47 CFR 80.1117 - Procedure for receipt and acknowledgement of distress alerts.

Code of Federal Regulations, 2012 CFR

2012-10-01

... radiotelephony of receipt of a distress alert from a ship station or a ship earth station must be given in the... telegraphy of receipt of a distress alert from a ship earth station must be given by the coast earth station... distress alerts. 80.1117 Section 80.1117 Telecommunication FEDERAL COMMUNICATIONS COMMISSION (CONTINUED...

37 CFR 256.2 - Royalty fee for compulsory license for secondary transmission by cable systems.

Code of Federal Regulations, 2013 CFR

2013-07-01

... receipts for the first distant signal equivalent; (3) .668 of 1 per centum of such gross receipts for each of the second, third and fourth distant signal equivalents; and (4) .314 of 1 per centum of such gross receipts for the fifth distant signal equivalent and each additional distant signal equivalent...

37 CFR 256.2 - Royalty fee for compulsory license for secondary transmission by cable systems.

Code of Federal Regulations, 2012 CFR

2012-07-01

... receipts for the first distant signal equivalent; (3) .668 of 1 per centum of such gross receipts for each of the second, third and fourth distant signal equivalents; and (4) .314 of 1 per centum of such gross receipts for the fifth distant signal equivalent and each additional distant signal equivalent...

37 CFR 256.2 - Royalty fee for compulsory license for secondary transmission by cable systems.

Code of Federal Regulations, 2011 CFR

2011-07-01

... receipts for the first distant signal equivalent; (3) .668 of 1 per centum of such gross receipts for each of the second, third and fourth distant signal equivalents; and (4) .314 of 1 per centum of such gross receipts for the fifth distant signal equivalent and each additional distant signal equivalent...

37 CFR 256.2 - Royalty fee for compulsory license for secondary transmission by cable systems.

Code of Federal Regulations, 2014 CFR

2014-07-01

... gross receipts for the first distant signal equivalent; (3) .668 of 1 per centum of such gross receipts for each of the second, third and fourth distant signal equivalents; and (4) .314 of 1 per centum of such gross receipts for the fifth distant signal equivalent and each additional distant signal...

37 CFR 256.2 - Royalty fee for compulsory license for secondary transmission by cable systems.

Code of Federal Regulations, 2010 CFR

2010-07-01

... receipts for the first distant signal equivalent; (3) .668 of 1 per centum of such gross receipts for each of the second, third and fourth distant signal equivalents; and (4) .314 of 1 per centum of such gross receipts for the fifth distant signal equivalent and each additional distant signal equivalent...

77 FR 75253 - Notice of Receipt of Kinder Morgan Cochin, LLC, Application for a Presidential Permit To Operate...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-19

... DEPARTMENT OF STATE [Public Notice: 8128] Notice of Receipt of Kinder Morgan Cochin, LLC... States and Canada AGENCY: Department of State. ACTION: Notice of Receipt of Kinder Morgan Cochin, LLC... States and Canada. SUMMARY: Notice is hereby given that the Department of State (DOS) has received from...

12 CFR 7.1015 - Receipt of stock from a small business investment company.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 12 Banks and Banking 1 2011-01-01 2011-01-01 false Receipt of stock from a small business... TREASURY BANK ACTIVITIES AND OPERATIONS Bank Powers § 7.1015 Receipt of stock from a small business investment company. A national bank may purchase the stock of a small business investment company (SBIC) (see...

13 CFR 121.104 - How does SBA calculate annual receipts?

Code of Federal Regulations, 2010 CFR

2010-01-01

...) Annual receipts of a concern that has been in business for three or more completed fiscal years means the...) Annual receipts of a concern which has been in business for less than three complete fiscal years means... business, multiplied by 52. (3) Where a concern has been in business three or more complete fiscal years...

Veneer-log production and receipts, North Central Region, 1972.

Treesearch

James E. Blyth

1974-01-01

Shows 1972 veneer-log production and receipts by species in the Lake States (Michigan, Minnesota, and Wisconsin) and in the Central States (Illinois, Indiana, Iowa, and Missouri). Comparisons are made with similar data for 1970. Includes tables showing veneer-log production and receipts (for selected years) since 1946 in the Lake States and since 1956 in the Central...

21 CFR 1271.265 - Receipt, predistribution shipment, and distribution of an HCT/P.

Code of Federal Regulations, 2011 CFR

2011-04-01

... and constructed to protect the HCT/P from contamination. For each type of HCT/P, you must establish... distribution of an HCT/P. 1271.265 Section 1271.265 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF... Practice § 1271.265 Receipt, predistribution shipment, and distribution of an HCT/P. (a) Receipt. You must...

Modeling loosely annotated images using both given and imagined annotations

NASA Astrophysics Data System (ADS)

Tang, Hong; Boujemaa, Nozha; Chen, Yunhao; Deng, Lei

2011-12-01

In this paper, we present an approach to learn latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: 1. ambiguous correspondences between visual features and annotated keywords; 2. incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning a topic model. In particular, some ``imagined'' keywords are poured into the incomplete annotation through measuring similarity between keywords in terms of their co-occurrence. Then, both given and imagined annotations are employed to learn probabilistic topic models for automatically annotating new images. We conduct experiments on two image databases (i.e., Corel and ESP) coupled with their loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods. The proposed method improves word-driven probability latent semantic analysis (PLSA-words) up to a comparable performance with the best discrete annotation method, while a merit of PLSA-words is still kept, i.e., a wider semantic range.

Bisphenol A in supermarket receipts and its exposure to human in Shenzhen, China.

PubMed

Lu, Shao-You; Chang, Wen-Jing; Sojinu, Samuel O; Ni, Hong-Gang

2013-08-01

Paper receipt has been documented as one major source of bisphenol A (BPA) for human exposure but little has been done by researchers to elaborate the potential health risk caused by handling paper receipt up to date. In the present study, BPA was analyzed in 42 supermarket receipts collected from Shenzhen, China. BPA was detected in all samples at concentrations ranging from 2.58 to 14.7mgg(-1). In most cases, the total amount of BPA on the receipt was at least one thousand times the amount found in the epoxy lining of a food can, another controversial use of the chemical. The estimated daily intakes (EDI) of BPA via handling of supermarket receipt ranged from 2 to 347μgday(-1) (mean, 40.4μgday(-1)) for a supermarket cashier and from 0.24 to 3.98μgday(-1) (mean, 0.69μgday(-1)) for general population. Based on the cumulative probability distribution of the calculated daily exposure to BPA via handling supermarket receipt, the EDI at the 0.1th and 1th percentile for supermarket cashier and general population, were already larger than 100ng (kgbw)(-1)day(-1), while at the 0.2th and 71th percentile, the EDI for both populations reached 1000ng (kgbw)(-1)day(-1). Considering the adverse endocrine disruptive effects of BPA and the dosage exposure level (from tens to hundreds ng (kgbw)(-1)day(-1)), human exposure to BPA in Shenzhen deserves more attention. Sensitivity analysis result showed that the handling time and frequency of supermarket receipts are the most important variables that contributed to most of the total variance of exposure. Copyright © 2013 Elsevier Ltd. All rights reserved.

[The Comparison of the Difference Between the Emphasis on and the Receipt of Patient Privacy in the Hospital Setting].

PubMed

Li, Chiu-Kuel; Lin, Chiou-Fen

2015-10-01

Privacy is a unique privilege for humans. Enhancing the balance between the importance given to patient privacy and the receipt of this privacy by patients is one key approach to improving the relationship between patients and the hospital. This study compared the difference between the importance of patient privacy and receipt of this privacy by patients as a reference for future patient privacy policy planning. This study was a cross-sectional design. We randomly sampled three hospitals in northern Taiwan and investigated patients using a questionnaire. The questionnaire was self-designed and verified for reliability and validity. We used frequency and percentage to describe demographic data and used a t-test to compare the deviation between the emphasis on and receipt of patient privacy. There were 296 valid samples in this study and the effective rate was 84.57%. The highest degree of importance was information privacy and the lowest was physical privacy. Physical privacy (t = 3.04, p < .001) and mental privacy (t = 2.42, p < .01) exhibited significant differences between emphasis and receipt. Demographic data on gender, age, education level, marital status, and occupation. Type of hospital and ward level correlated with the emphasis and receipt of privacy. The importance of privacy for physical and mental wellbeing was higher than the actual receipt of this privacy among the patient sample. The importance of privacy for married individuals and young women with high education levels was higher, while males and less-educated individuals scored lower in terms of privacy receipt. Medical agencies must provide higher levels of physical and mental privacy in order to enhance patient satisfaction.

Development of a database of health insurance claims: standardization of disease classifications and anonymous record linkage.

PubMed

Kimura, Shinya; Sato, Toshihiko; Ikeda, Shunya; Noda, Mitsuhiko; Nakayama, Takeo

2010-01-01

Health insurance claims (ie, receipts) record patient health care treatments and expenses and, although created for the health care payment system, are potentially useful for research. Combining different types of receipts generated for the same patient would dramatically increase the utility of these receipts. However, technical problems, including standardization of disease names and classifications, and anonymous linkage of individual receipts, must be addressed. In collaboration with health insurance societies, all information from receipts (inpatient, outpatient, and pharmacy) was collected. To standardize disease names and classifications, we developed a computer-aided post-entry standardization method using a disease name dictionary based on International Classification of Diseases (ICD)-10 classifications. We also developed an anonymous linkage system by using an encryption code generated from a combination of hash values and stream ciphers. Using different sets of the original data (data set 1: insurance certificate number, name, and sex; data set 2: insurance certificate number, date of birth, and relationship status), we compared the percentage of successful record matches obtained by using data set 1 to generate key codes with the percentage obtained when both data sets were used. The dictionary's automatic conversion of disease names successfully standardized 98.1% of approximately 2 million new receipts entered into the database. The percentage of anonymous matches was higher for the combined data sets (98.0%) than for data set 1 (88.5%). The use of standardized disease classifications and anonymous record linkage substantially contributed to the construction of a large, chronologically organized database of receipts. This database is expected to aid in epidemiologic and health services research using receipt information.

TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes

PubMed Central

Leroy, Philippe; Guilhot, Nicolas; Sakai, Hiroaki; Bernard, Aurélien; Choulet, Frédéric; Theil, Sébastien; Reboux, Sébastien; Amano, Naoki; Flutre, Timothée; Pelegrin, Céline; Ohyanagi, Hajime; Seidel, Michael; Giacomoni, Franck; Reichstadt, Mathieu; Alaux, Michael; Gicquello, Emmanuelle; Legeai, Fabrice; Cerutti, Lorenzo; Numa, Hisataka; Tanaka, Tsuyoshi; Mayer, Klaus; Itoh, Takeshi; Quesneville, Hadi; Feuillet, Catherine

2012-01-01

In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. PMID:22645565

Effects of receipt of Social Security retirement benefits on older women's employment.

PubMed

Gillen, Martie; Heath, Claudia J

2017-01-01

Labor force participation of women has declined since 1999; however, labor force participation of women 62+ has increased. The 2000-2006 waves of Health and Retirement Study (HRS) data, the initial years of the continuing upward trajectory, were used to test the effects of receipt of Social Security retirement benefits on older women's employment. The models tested: (a) the effect of receipt of Social Security retirement benefits on whether employed; and (b) for women receiving Social Security retirement benefits, the effect of age elected receipt of benefits on whether employed. Both models included the effects of human capital characteristics and income sources. Receipt of Social Security benefits, pension income, and current age reduced the likelihood of employment; while educational level, good to excellent health, and nonmarried marital status increased the likelihood of employment. The older the woman was when she elected Social Security benefits, the more likely she was to be employed.

EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

PubMed Central

Thibaud-Nissen, Françoise; Campbell, Matthew; Hamilton, John P; Zhu, Wei; Buell, C Robin

2007-01-01

Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation) is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation. This requires tools that facilitate 1) the submission of gene annotation to an annotation project, 2) the review of the submitted models by project annotators, and 3) the incorporation of the submitted models in the ongoing annotation effort. Results We have developed the Eukaryotic Community Annotation Package (EuCAP), an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA) has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs) in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website , as well as in the Community Annotation track of the Genome Browser. Conclusion We have applied EuCAP to rice. As of July 2007, the structural and/or functional annotation of 1,094 genes representing 57 families have been deposited and integrated into the current gene set. All of the EuCAP components are open-source, thereby allowing the implementation of EuCAP for the annotation of other genomes. EuCAP is available at . PMID:17961238

Annotated chemical patent corpus: a gold standard for text mining.

PubMed

Akhondi, Saber A; Klenner, Alexander G; Tyrchan, Christian; Manchala, Anil K; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A R P; Sayle, Roger; Kors, Jan A; Muresan, Sorel

2014-01-01

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

Annotated Chemical Patent Corpus: A Gold Standard for Text Mining

PubMed Central

Akhondi, Saber A.; Klenner, Alexander G.; Tyrchan, Christian; Manchala, Anil K.; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A. R. P.; Sayle, Roger; Kors, Jan A.; Muresan, Sorel

2014-01-01

Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org. PMID:25268232

48 CFR 52.229-10 - State of New Mexico Gross Receipts and Compensating Tax.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 48 Federal Acquisition Regulations System 2 2010-10-01 2010-10-01 false State of New Mexico Gross... Provisions and Clauses 52.229-10 State of New Mexico Gross Receipts and Compensating Tax. As prescribed in 29.401-4(b), insert the following clause: State of New Mexico Gross Receipts and Compensating Tax (APR...

49 CFR 375.701 - May I provide for a release of liability on my delivery receipt?

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 5 2010-10-01 2010-10-01 false May I provide for a release of liability on my... REGULATIONS Delivery of Shipments § 375.701 May I provide for a release of liability on my delivery receipt? (a) Your delivery receipt or shipping document must not contain any language purporting to release or...

76 FR 75598 - 60-Day Notice of Proposed Information Collection: DS-86, Statement of Non-Receipt of a Passport...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-02

..., Statement of Non-Receipt of a Passport, 1405-0146 ACTION: Notice of request for public comments. SUMMARY... Reduction Act of 1995. Title of Information Collection: Statement of Non-Receipt of a Passport. OMB Control... received the passport for which they originally applied. Estimated Number of Respondents: 12,755 per year...

26 CFR 1.1031(b)-1 - Receipt of other property or money in tax-free exchange.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 26 Internal Revenue 11 2014-04-01 2014-04-01 false Receipt of other property or money in tax-free...)-1 Receipt of other property or money in tax-free exchange. (a) If the taxpayer receives other property (in addition to property permitted to be received without recognition of gain) or money— (1) In an...

26 CFR 1.1031(b)-1 - Receipt of other property or money in tax-free exchange.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 26 Internal Revenue 11 2013-04-01 2013-04-01 false Receipt of other property or money in tax-free...)-1 Receipt of other property or money in tax-free exchange. (a) If the taxpayer receives other property (in addition to property permitted to be received without recognition of gain) or money— (1) In an...

26 CFR 1.1031(b)-1 - Receipt of other property or money in tax-free exchange.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 11 2011-04-01 2011-04-01 false Receipt of other property or money in tax-free...)-1 Receipt of other property or money in tax-free exchange. (a) If the taxpayer receives other property (in addition to property permitted to be received without recognition of gain) or money— (1) In an...

26 CFR 1.1031(b)-1 - Receipt of other property or money in tax-free exchange.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 26 Internal Revenue 11 2012-04-01 2012-04-01 false Receipt of other property or money in tax-free...)-1 Receipt of other property or money in tax-free exchange. (a) If the taxpayer receives other property (in addition to property permitted to be received without recognition of gain) or money— (1) In an...

75 FR 39971 - Notice of Delegation of Authority to Secretary to the Commission To Publish Notice of the Receipt...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-07-13

... Publish Notice of the Receipt of Complaints Under Section 337 of the Tariff Act of 1930 and To Solicit... authority to the Secretary to the Commission to publish notice of the receipt of future complaints under... has determined to delegate to the Secretary to the Commission the authority to publish notice of...

75 FR 60444 - Certain New Chemicals; Receipt and Status Information

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-30

...- adhesives dimethyl-3-[(1- oxododecyl)oxy]propy lidene] amino]methylethyl]- .omega.-[2-[[2,2- dimethyl-3-[(1... sections 5(d)(2) and 5(d)(3) of TSCA, EPA is required to publish a notice of receipt of a premanufacture...)(2) and 5(d)(3) of TSCA, EPA is required to publish a notice of receipt of a PMN or an application...

48 CFR 52.229-10 - State of New Mexico Gross Receipts and Compensating Tax.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 2 2013-10-01 2013-10-01 false State of New Mexico Gross... Provisions and Clauses 52.229-10 State of New Mexico Gross Receipts and Compensating Tax. As prescribed in 29.401-4(b), insert the following clause: State of New Mexico Gross Receipts and Compensating Tax (APR...

48 CFR 52.229-10 - State of New Mexico Gross Receipts and Compensating Tax.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 2 2014-10-01 2014-10-01 false State of New Mexico Gross... Provisions and Clauses 52.229-10 State of New Mexico Gross Receipts and Compensating Tax. As prescribed in 29.401-4(b), insert the following clause: State of New Mexico Gross Receipts and Compensating Tax (APR...

48 CFR 52.229-10 - State of New Mexico Gross Receipts and Compensating Tax.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 2 2011-10-01 2011-10-01 false State of New Mexico Gross... Provisions and Clauses 52.229-10 State of New Mexico Gross Receipts and Compensating Tax. As prescribed in 29.401-4(b), insert the following clause: State of New Mexico Gross Receipts and Compensating Tax (APR...

48 CFR 52.229-10 - State of New Mexico Gross Receipts and Compensating Tax.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 2 2012-10-01 2012-10-01 false State of New Mexico Gross... Provisions and Clauses 52.229-10 State of New Mexico Gross Receipts and Compensating Tax. As prescribed in 29.401-4(b), insert the following clause: State of New Mexico Gross Receipts and Compensating Tax (APR...

7 CFR 982.467 - Report of receipts and dispositions of hazelnuts grown outside the United States.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 8 2010-01-01 2010-01-01 false Report of receipts and dispositions of hazelnuts grown... Regulations § 982.467 Report of receipts and dispositions of hazelnuts grown outside the United States. Each handler who receives hazelnuts grown outside the United States shall report to the Board monthly on F/H...

7 CFR 982.467 - Report of receipts and dispositions of hazelnuts grown outside the United States.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 8 2011-01-01 2011-01-01 false Report of receipts and dispositions of hazelnuts grown... Regulations § 982.467 Report of receipts and dispositions of hazelnuts grown outside the United States. Each handler who receives hazelnuts grown outside the United States shall report to the Board monthly on F/H...

How equitable is the uptake of conditional cash transfers for maternity care in India? Evidence from the Janani Suraksha Yojana scheme in Odisha and Jharkhand.

PubMed

Thongkong, Nattawut; van de Poel, Ellen; Roy, Swati Sarbani; Rath, Shibanand; Houweling, Tanja A J

2017-03-10

In 2005, the Indian Government introduced the Janani Suraksha Yojana (JSY) scheme - a conditional cash transfer program that incentivizes women to deliver in a health facility - in order to reduce maternal and neonatal mortality. Our study aimed to measure and explain socioeconomic inequality in the receipt of JSY benefits. We used prospectively collected data on 3,682 births (in 2009-2010) from a demographic surveillance system in five districts in Jharkhand and Odisha state, India. Linear probability models were used to identify the determinants of receipt of JSY benefits. Poor-rich inequality in the receipt of JSY benefits was measured by a corrected concentration index (CI), and the most important drivers of this inequality were identified using decomposition techniques. While the majority of women had heard of the scheme (94% in Odisha, 85% in Jharkhand), receipt of JSY benefits was comparatively low (62% in Odisha, 20% in Jharkhand). Receipt of the benefits was highly variable by district, especially in Jharkhand, where 5% of women in Godda district received the benefits, compared with 40% of women in Ranchi district. There were substantial pro-rich inequalities in JSY receipt (CI 0.10, standard deviation (SD) 0.03 in Odisha; CI 0.18, SD 0.02 in Jharkhand) and in the institutional delivery rate (CI 0.16, SD 0.03 in Odisha; CI 0.30, SD 0.02 in Jharkhand). Delivery in a public facility was an important determinant of receipt of JSY benefits and explained a substantial part of the observed poor-rich inequalities in receipt of the benefits. Yet, even among public facility births in Jharkhand, pro-rich inequality in JSY receipt was substantial (CI 0.14, SD 0.05). This was largely explained by district-level differences in wealth and JSY receipt. Conversely, in Odisha, poorer women delivering in a government institution were at least as likely to receive JSY benefits as richer women (CI -0.05, SD 0.03). JSY benefits were not equally distributed, favouring wealthier groups. These inequalities in turn reflected pro-rich inequalities in the institutional delivery. The JSY scheme is currently not sufficient to close the poor-rich gap in institutional delivery rate. Important barriers to institutional delivery remain to be addressed and more support is needed for low performing districts and states.

From Data to Knowledge – Promising Analytical Tools and Techniques for Capture and Reuse of Corporate Knowledge and to Aid in the State Evaluation Process

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

Danielson, Gary R.; Augustenborg, Elsa C.; Beck, Andrew E.

2010-10-29

The IAEA is challenged with limited availability of human resources for inspection and data analysis while proliferation threats increase. PNNL has a variety of IT solutions and techniques (at varying levels of maturity and development) that take raw data closer to useful knowledge, thereby assisting with and standardizing the analytical processes. This paper highlights some PNNL tools and techniques which are applicable to the international safeguards community, including: • Intelligent in-situ triage of data prior to reliable transmission to an analysis center resulting in the transmission of smaller and more relevant data sets • Capture of expert knowledge in re-usablemore » search strings tailored to specific mission outcomes • Image based searching fused with text based searching • Use of gaming to discover unexpected proliferation scenarios • Process modeling (e.g. Physical Model) as the basis for an information integration portal, which links to data storage locations along with analyst annotations, categorizations, geographic data, search strings and visualization outputs.« less

A top-level ontology of functions and its application in the Open Biomedical Ontologies.

PubMed

Burek, Patryk; Hoehndorf, Robert; Loebe, Frank; Visagie, Johann; Herre, Heinrich; Kelso, Janet

2006-07-15

A clear understanding of functions in biology is a key component in accurate modelling of molecular, cellular and organismal biology. Using the existing biomedical ontologies it has been impossible to capture the complexity of the community's knowledge about biological functions. We present here a top-level ontological framework for representing knowledge about biological functions. This framework lends greater accuracy, power and expressiveness to biomedical ontologies by providing a means to capture existing functional knowledge in a more formal manner. An initial major application of the ontology of functions is the provision of a principled way in which to curate functional knowledge and annotations in biomedical ontologies. Further potential applications include the facilitation of ontology interoperability and automated reasoning. A major advantage of the proposed implementation is that it is an extension to existing biomedical ontologies, and can be applied without substantial changes to these domain ontologies. The Ontology of Functions (OF) can be downloaded in OWL format from http://onto.eva.mpg.de/. Additionally, a UML profile and supplementary information and guides for using the OF can be accessed from the same website.

Evaluating Computational Gene Ontology Annotations.

PubMed

Škunca, Nives; Roberts, Richard J; Steffen, Martin

2017-01-01

Two avenues to understanding gene function are complementary and often overlapping: experimental work and computational prediction. While experimental annotation generally produces high-quality annotations, it is low throughput. Conversely, computational annotations have broad coverage, but the quality of annotations may be variable, and therefore evaluating the quality of computational annotations is a critical concern.In this chapter, we provide an overview of strategies to evaluate the quality of computational annotations. First, we discuss why evaluating quality in this setting is not trivial. We highlight the various issues that threaten to bias the evaluation of computational annotations, most of which stem from the incompleteness of biological databases. Second, we discuss solutions that address these issues, for example, targeted selection of new experimental annotations and leveraging the existing experimental annotations.

BEACON: automated tool for Bacterial GEnome Annotation ComparisON.

PubMed

Kalkatawi, Manal; Alam, Intikhab; Bajic, Vladimir B

2015-08-18

Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON's utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27%, while the number of genes without any function assignment is reduced. We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/ .

Outpatient Rehabilitation for Medicaid-Insured Children Hospitalized With Traumatic Brain Injury

PubMed Central

Symons, Rebecca G.; Wang, Jin; Ebel, Beth H.; Vavilala, Monica S.; Buchwald, Dedra; Temkin, Nancy; Jaffe, Kenneth M.; Rivara, Frederick P.

2016-01-01

OBJECTIVES: To describe the prevalence of postdischarge outpatient rehabilitation among Medicaid-insured children hospitalized with a traumatic brain injury (TBI) and to identify factors associated with receipt of services. METHODS: Retrospective cohort of children <21 years, hospitalized for a TBI between 2007 and 2012, from a national Medicaid claims database. Outcome measures were receipt of outpatient rehabilitation (physical, occupational, or speech therapies or physician visits to a rehabilitation provider) 1 and 3 years after discharge. Multivariable regression analyses determined the association of demographic variables, injury severity, and receipt of inpatient services with receipt of outpatient rehabilitation at 1 and 3 years. The mean number of services was compared between racial/ethnic groups. RESULTS: Among 9361 children, only 29% received any type of outpatient rehabilitation therapy during the first year after injury, although 62% sustained a moderate to severe TBI. The proportion of children receiving outpatient therapies declined to 12% in the second and third years. The most important predictor of receipt of outpatient rehabilitation was receipt of inpatient therapies or consultation with a rehabilitation physician during acute care. Compared with children of other racial/ethnic groups, Hispanic children had lower rates of receipt of outpatient speech therapy. CONCLUSIONS: Hospitalized children who received inpatient assessment of rehabilitation needs were more likely to continue outpatient rehabilitation care. Hispanic children with TBI were less likely than non-Hispanics to receive speech therapy. Interventions to increase inpatient rehabilitation during acute care might increase outpatient rehabilitation and improve outcomes for all children. PMID:27244850

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

PubMed

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

2011-01-22

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

Final Technical Report - Use of Systems Biology Approaches to Develop Advanced Biofuel-Synthesizing Cyanobacterial Strains

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

Pakrasi, Himadri

The overall objective of this project was to use a systems biology approach to evaluate the potentials of a number of cyanobacterial strains for photobiological production of advanced biofuels and/or their chemical precursors. Cyanobacteria are oxygen evolving photosynthetic prokaryotes. Among them, certain unicellular species such as Cyanothece can also fix N 2, a process that is exquisitely sensitive to oxygen. To accommodate such incompatible processes in a single cell, Cyanothece produces oxygen during the day, and creates an O 2-limited intracellular environment during the night to perform O 2-sensitive processes such as N 2-fixation. Thus, Cyanothece cells are natural bioreactorsmore » for the storage of captured solar energy with subsequent utilization at a different time during a diurnal cycle. Our studies include the identification of a novel, fast-growing, mixotrophic, transformable cyanobacterium. This strain has been sequenced and will be made available to the community. In addition, we have developed genome-scale models for a family of cyanobacteria to assess their metabolic repertoire. Furthermore, we developed a method for rapid construction of metabolic models using multiple annotation sources and a metabolic model of a related organism. This method will allow rapid annotation and screening of potential phenotypes based on the newly available genome sequences of many organisms.« less

Large-scale gene function analysis with the PANTHER classification system.

PubMed

Mi, Huaiyu; Muruganujan, Anushya; Casagrande, John T; Thomas, Paul D

2013-08-01

The PANTHER (protein annotation through evolutionary relationship) classification system (http://www.pantherdb.org/) is a comprehensive system that combines gene function, ontology, pathways and statistical analysis tools that enable biologists to analyze large-scale, genome-wide data from sequencing, proteomics or gene expression experiments. The system is built with 82 complete genomes organized into gene families and subfamilies, and their evolutionary relationships are captured in phylogenetic trees, multiple sequence alignments and statistical models (hidden Markov models or HMMs). Genes are classified according to their function in several different ways: families and subfamilies are annotated with ontology terms (Gene Ontology (GO) and PANTHER protein class), and sequences are assigned to PANTHER pathways. The PANTHER website includes a suite of tools that enable users to browse and query gene functions, and to analyze large-scale experimental data with a number of statistical tests. It is widely used by bench scientists, bioinformaticians, computer scientists and systems biologists. In the 2013 release of PANTHER (v.8.0), in addition to an update of the data content, we redesigned the website interface to improve both user experience and the system's analytical capability. This protocol provides a detailed description of how to analyze genome-wide experimental data with the PANTHER classification system.

Shared periodic performer movements coordinate interactions in duo improvisations

PubMed Central

Jakubowski, Kelly; Moran, Nikki; Keller, Peter E.

2018-01-01

Human interaction involves the exchange of temporally coordinated, multimodal cues. Our work focused on interaction in the visual domain, using music performance as a case for analysis due to its temporally diverse and hierarchical structures. We made use of two improvising duo datasets—(i) performances of a jazz standard with a regular pulse and (ii) non-pulsed, free improvizations—to investigate whether human judgements of moments of interaction between co-performers are influenced by body movement coordination at multiple timescales. Bouts of interaction in the performances were manually annotated by experts and the performers’ movements were quantified using computer vision techniques. The annotated interaction bouts were then predicted using several quantitative movement and audio features. Over 80% of the interaction bouts were successfully predicted by a broadband measure of the energy of the cross-wavelet transform of the co-performers’ movements in non-pulsed duos. A more complex model, with multiple predictors that captured more specific, interacting features of the movements, was needed to explain a significant amount of variance in the pulsed duos. The methods developed here have key implications for future work on measuring visual coordination in musical ensemble performances, and can be easily adapted to other musical contexts, ensemble types and traditions. PMID:29515867

Improving the representation of peptide-like inhibitor and antibiotic molecules in the Protein Data Bank

PubMed Central

Dutta, Shuchismita; Dimitropoulos, Dimitris; Feng, Zukang; Persikova, Irina; Sen, Sanchayita; Shao, Chenghua; Westbrook, John; Young, Jasmine; Zhuravleva, Marina A; Kleywegt, Gerard J; Berman, Helen M

2014-01-01

With the accumulation of a large number and variety of molecules in the Protein Data Bank (PDB) comes the need on occasion to review and improve their representation. The Worldwide PDB (wwPDB) partners have periodically updated various aspects of structural data representation to improve the integrity and consistency of the archive. The remediation effort described here was focused on improving the representation of peptide-like inhibitor and antibiotic molecules so that they can be easily identified and analyzed. Peptide-like inhibitors or antibiotics were identified in over 1000 PDB entries, systematically reviewed and represented either as peptides with polymer sequence or as single components. For the majority of the single-component molecules, their peptide-like composition was captured in a new representation, called the subcomponent sequence. A novel concept called “group” was developed for representing complex peptide-like antibiotics and inhibitors that are composed of multiple polymer and nonpolymer components. In addition, a reference dictionary was developed with detailed information about these peptide-like molecules to aid in their annotation, identification and analysis. Based on the experience gained in this remediation, guidelines, procedures, and tools were developed to annotate new depositions containing peptide-like inhibitors and antibiotics accurately and consistently. © 2013 Wiley Periodicals, Inc. Biopolymers 101: 659–668, 2014. PMID:24173824

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC

PubMed Central

Clematide, Simon; Akhondi, Saber A; van Mulligen, Erik M; Rebholz-Schuhmann, Dietrich

2015-01-01

Objective To create a multilingual gold-standard corpus for biomedical concept recognition. Materials and methods We selected text units from different parallel corpora (Medline abstract titles, drug labels, biomedical patent claims) in English, French, German, Spanish, and Dutch. Three annotators per language independently annotated the biomedical concepts, based on a subset of the Unified Medical Language System and covering a wide range of semantic groups. To reduce the annotation workload, automatically generated preannotations were provided. Individual annotations were automatically harmonized and then adjudicated, and cross-language consistency checks were carried out to arrive at the final annotations. Results The number of final annotations was 5530. Inter-annotator agreement scores indicate good agreement (median F-score 0.79), and are similar to those between individual annotators and the gold standard. The automatically generated harmonized annotation set for each language performed equally well as the best annotator for that language. Discussion The use of automatic preannotations, harmonized annotations, and parallel corpora helped to keep the manual annotation efforts manageable. The inter-annotator agreement scores provide a reference standard for gauging the performance of automatic annotation techniques. Conclusion To our knowledge, this is the first gold-standard corpus for biomedical concept recognition in languages other than English. Other distinguishing features are the wide variety of semantic groups that are being covered, and the diversity of text genres that were annotated. PMID:25948699

The 3D Human Motion Control Through Refined Video Gesture Annotation

NASA Astrophysics Data System (ADS)

Jin, Yohan; Suk, Myunghoon; Prabhakaran, B.

In the beginning of computer and video game industry, simple game controllers consisting of buttons and joysticks were employed, but recently game consoles are replacing joystick buttons with novel interfaces such as the remote controllers with motion sensing technology on the Nintendo Wii [1] Especially video-based human computer interaction (HCI) technique has been applied to games, and the representative game is 'Eyetoy' on the Sony PlayStation 2. Video-based HCI technique has great benefit to release players from the intractable game controller. Moreover, in order to communicate between humans and computers, video-based HCI is very crucial since it is intuitive, easy to get, and inexpensive. On the one hand, extracting semantic low-level features from video human motion data is still a major challenge. The level of accuracy is really dependent on each subject's characteristic and environmental noises. Of late, people have been using 3D motion-capture data for visualizing real human motions in 3D space (e.g, 'Tiger Woods' in EA Sports, 'Angelina Jolie' in Bear-Wolf movie) and analyzing motions for specific performance (e.g, 'golf swing' and 'walking'). 3D motion-capture system ('VICON') generates a matrix for each motion clip. Here, a column is corresponding to a human's sub-body part and row represents time frames of data capture. Thus, we can extract sub-body part's motion only by selecting specific columns. Different from low-level feature values of video human motion, 3D human motion-capture data matrix are not pixel values, but is closer to human level of semantics.

A review of randomized controlled trials comparing the effectiveness of hand held computers with paper methods for data collection

PubMed Central

Lane, Shannon J; Heddle, Nancy M; Arnold, Emmy; Walker, Irwin

2006-01-01

Background Handheld computers are increasingly favoured over paper and pencil methods to capture data in clinical research. Methods This study systematically identified and reviewed randomized controlled trials (RCTs) that compared the two methods for self-recording and reporting data, and where at least one of the following outcomes was assessed: data accuracy; timeliness of data capture; and adherence to protocols for data collection. Results A comprehensive key word search of NLM Gateway's database yielded 9 studies fitting the criteria for inclusion. Data extraction was performed and checked by two of the authors. None of the studies included all outcomes. The results overall, favor handheld computers over paper and pencil for data collection among study participants but the data are not uniform for the different outcomes. Handheld computers appear superior in timeliness of receipt and data handling (four of four studies) and are preferred by most subjects (three of four studies). On the other hand, only one of the trials adequately compared adherence to instructions for recording and submission of data (handheld computers were superior), and comparisons of accuracy were inconsistent between five studies. Conclusion Handhelds are an effective alternative to paper and pencil modes of data collection; they are faster and were preferred by most users. PMID:16737535

76 FR 32019 - Notice of Receipt of Petition for Decision That Nonconforming 2008-2010 M&V GmbH Siegmar Fzb...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-06-02

...-0062; Notice 1] Notice of Receipt of Petition for Decision That Nonconforming 2008-2010 M&V GmbH..., DOT. ACTION: Notice of receipt of petition for decision that nonconforming 2008-2010 M&V GmbH Siegmar... Highway Traffic Safety Administration (NHTSA) of a petition for a decision that 2008-2010 M&V GmbH Siegmar...

11 CFR 103.3 - Deposit of receipts and disbursements (2 U.S.C. 432(h)(1)).

Code of Federal Regulations, 2010 CFR

2010-01-01

... forth in 11 CFR 110.1 or 110.2, and contributions which do not appear to be excessive on their face, but... receipts by a political committee shall be deposited in account(s) established pursuant to 11 CFR 103.2, except that any contribution may be, within 10 days of the treasurer's receipt, returned to the...

26 CFR 1.312-8 - Effect on earnings and profits of receipt of tax-free distributions requiring adjustment or...

Code of Federal Regulations, 2011 CFR

2011-04-01

... 26 Internal Revenue 4 2011-04-01 2011-04-01 false Effect on earnings and profits of receipt of tax...) INCOME TAXES Effects on Corporation § 1.312-8 Effect on earnings and profits of receipt of tax-free... earnings and profits, where a corporation receives (after February 28, 1913) from a second corporation a...

26 CFR 1.312-8 - Effect on earnings and profits of receipt of tax-free distributions requiring adjustment or...

Code of Federal Regulations, 2010 CFR

2010-04-01

... 26 Internal Revenue 4 2010-04-01 2010-04-01 false Effect on earnings and profits of receipt of tax...) INCOME TAXES Effects on Corporation § 1.312-8 Effect on earnings and profits of receipt of tax-free... earnings and profits, where a corporation receives (after February 28, 1913) from a second corporation a...

United States pulpwood receipts : softwood and hardwood, roundwood and residues, 1950-1996

Treesearch

C. Denise Ingram; Peter J. Ince; Ryan L. Mehlberg

1999-01-01

This report shows pulpwood receipts at wood pulp mills in the United States for the period 1950 to 1996. It is an update of the General Technical Report FPL1GTR173, bUnited States Pulpwood Receipts: Softwood and Hardwood, Roundwood and Residues, 195011989,c published in 1993. This report continues as a compilation of published and estimated data based on information...

Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome

PubMed Central

2010-01-01

Background A goal of the Bovine Genome Database (BGD; http://BovineGenome.org) has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC) in the annotation and analysis of the bovine genome. We were faced with several challenges, including the need to maintain consistent quality despite diversity in annotation expertise in the research community, the need to maintain consistent data formats, and the need to minimize the potential duplication of annotation effort. With new sequencing technologies allowing many more eukaryotic genomes to be sequenced, the demand for collaborative annotation is likely to increase. Here we present our approach, challenges and solutions facilitating a large distributed annotation project. Results and Discussion BGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD. Conclusions We have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence. PMID:21092105

Building a comprehensive syntactic and semantic corpus of Chinese clinical texts.

PubMed

He, Bin; Dong, Bin; Guan, Yi; Yang, Jinfeng; Jiang, Zhipeng; Yu, Qiubin; Cheng, Jianyi; Qu, Chunyan

2017-05-01

To build a comprehensive corpus covering syntactic and semantic annotations of Chinese clinical texts with corresponding annotation guidelines and methods as well as to develop tools trained on the annotated corpus, which supplies baselines for research on Chinese texts in the clinical domain. An iterative annotation method was proposed to train annotators and to develop annotation guidelines. Then, by using annotation quality assurance measures, a comprehensive corpus was built, containing annotations of part-of-speech (POS) tags, syntactic tags, entities, assertions, and relations. Inter-annotator agreement (IAA) was calculated to evaluate the annotation quality and a Chinese clinical text processing and information extraction system (CCTPIES) was developed based on our annotated corpus. The syntactic corpus consists of 138 Chinese clinical documents with 47,426 tokens and 2612 full parsing trees, while the semantic corpus includes 992 documents that annotated 39,511 entities with their assertions and 7693 relations. IAA evaluation shows that this comprehensive corpus is of good quality, and the system modules are effective. The annotated corpus makes a considerable contribution to natural language processing (NLP) research into Chinese texts in the clinical domain. However, this corpus has a number of limitations. Some additional types of clinical text should be introduced to improve corpus coverage and active learning methods should be utilized to promote annotation efficiency. In this study, several annotation guidelines and an annotation method for Chinese clinical texts were proposed, and a comprehensive corpus with its NLP modules were constructed, providing a foundation for further study of applying NLP techniques to Chinese texts in the clinical domain. Copyright © 2017. Published by Elsevier Inc.

A Targeted Capture Linkage Map Anchors the Genome of the Schistosomiasis Vector Snail, Biomphalaria glabrata.

PubMed

Tennessen, Jacob A; Bollmann, Stephanie R; Blouin, Michael S

2017-07-05

The aquatic planorbid snail Biomphalaria glabrata is one of the most intensively-studied mollusks due to its role in the transmission of schistosomiasis. Its 916 Mb genome has recently been sequenced and annotated, but it remains poorly assembled. Here, we used targeted capture markers to map over 10,000 B. glabrata scaffolds in a linkage cross of 94 F1 offspring, generating 24 linkage groups (LGs). We added additional scaffolds to these LGs based on linkage disequilibrium (LD) analysis of targeted capture and whole-genome sequences of 96 unrelated snails. Our final linkage map consists of 18,613 scaffolds comprising 515 Mb, representing 56% of the genome and 75% of genic and nonrepetitive regions. There are 18 large (> 10 Mb) LGs, likely representing the expected 18 haploid chromosomes, and > 50% of the genome has been assigned to LGs of at least 17 Mb. Comparisons with other gastropod genomes reveal patterns of synteny and chromosomal rearrangements. Linkage relationships of key immune-relevant genes may help clarify snail-schistosome interactions. By focusing on linkage among genic and nonrepetitive regions, we have generated a useful resource for associating snail phenotypes with causal genes, even in the absence of a complete genome assembly. A similar approach could potentially improve numerous poorly-assembled genomes in other taxa. This map will facilitate future work on this host of a serious human parasite. Copyright © 2017 Tennessen et al.

Hypertext Annotation: Effects of Presentation Formats and Learner Proficiency on Reading Comprehension and Vocabulary Learning in Foreign Languages

ERIC Educational Resources Information Center

Chen, I-Jung; Yen, Jung-Chuan

2013-01-01

This study extends current knowledge by exploring the effect of different annotation formats, namely in-text annotation, glossary annotation, and pop-up annotation, on hypertext reading comprehension in a foreign language and vocabulary acquisition across student proficiencies. User attitudes toward the annotation presentation were also…

An approach to describing and analysing bulk biological annotation quality: a case study using UniProtKB.

PubMed

Bell, Michael J; Gillespie, Colin S; Swan, Daniel; Lord, Phillip

2012-09-15

Annotations are a key feature of many biological databases, used to convey our knowledge of a sequence to the reader. Ideally, annotations are curated manually, however manual curation is costly, time consuming and requires expert knowledge and training. Given these issues and the exponential increase of data, many databases implement automated annotation pipelines in an attempt to avoid un-annotated entries. Both manual and automated annotations vary in quality between databases and annotators, making assessment of annotation reliability problematic for users. The community lacks a generic measure for determining annotation quality and correctness, which we look at addressing within this article. Specifically we investigate word reuse within bulk textual annotations and relate this to Zipf's Principle of Least Effort. We use the UniProt Knowledgebase (UniProtKB) as a case study to demonstrate this approach since it allows us to compare annotation change, both over time and between automated and manually curated annotations. By applying power-law distributions to word reuse in annotation, we show clear trends in UniProtKB over time, which are consistent with existing studies of quality on free text English. Further, we show a clear distinction between manual and automated analysis and investigate cohorts of protein records as they mature. These results suggest that this approach holds distinct promise as a mechanism for judging annotation quality. Source code is available at the authors website: http://homepages.cs.ncl.ac.uk/m.j.bell1/annotation. phillip.lord@newcastle.ac.uk.

A multilingual gold-standard corpus for biomedical concept recognition: the Mantra GSC.

PubMed

Kors, Jan A; Clematide, Simon; Akhondi, Saber A; van Mulligen, Erik M; Rebholz-Schuhmann, Dietrich

2015-09-01

To create a multilingual gold-standard corpus for biomedical concept recognition. We selected text units from different parallel corpora (Medline abstract titles, drug labels, biomedical patent claims) in English, French, German, Spanish, and Dutch. Three annotators per language independently annotated the biomedical concepts, based on a subset of the Unified Medical Language System and covering a wide range of semantic groups. To reduce the annotation workload, automatically generated preannotations were provided. Individual annotations were automatically harmonized and then adjudicated, and cross-language consistency checks were carried out to arrive at the final annotations. The number of final annotations was 5530. Inter-annotator agreement scores indicate good agreement (median F-score 0.79), and are similar to those between individual annotators and the gold standard. The automatically generated harmonized annotation set for each language performed equally well as the best annotator for that language. The use of automatic preannotations, harmonized annotations, and parallel corpora helped to keep the manual annotation efforts manageable. The inter-annotator agreement scores provide a reference standard for gauging the performance of automatic annotation techniques. To our knowledge, this is the first gold-standard corpus for biomedical concept recognition in languages other than English. Other distinguishing features are the wide variety of semantic groups that are being covered, and the diversity of text genres that were annotated. © The Author 2015. Published by Oxford University Press on behalf of the American Medical Informatics Association.

Satisfaction with the humanitarian response to the 2010 Pakistan floods: a call for increased accountability to beneficiaries.

PubMed

Kirsch, Thomas; Siddiqui, Muhammad Ahmed; Perrin, Paul Clayton; Robinson, W Courtland; Sauer, Lauren M; Doocy, Shannon

2013-07-01

Ascertain recipients' level of satisfaction with humanitarian response efforts. A multi-stage, 80×20 cluster sample randomized survey (1800 households) with probability proportional to size of households affected by the 2010 Indus river floods in Pakistan. The floods affected over 18 million households and led to more than 8 billion USD in response dollars. Less than 20% of respondents reported being satisfied with response, though a small increase in satisfaction levels was observed over the three time periods of interest. Within the first month, receipt of hygiene items, food and household items was most strongly predictive of overall satisfaction. At 6 months, positive receipt of medicines was also highly predictive of satisfaction. The proportion of households reporting unmet needs remained elevated throughout the 6-month period following the floods and varied from 50% to 80%. Needs were best met between 1 and 3 months postflood, when response was at its peak. Unmet needs were the greatest at 6 months, when response was being phased down. Access-limiting issues were rarely captured during routine monitoring and evaluation efforts and seem to be a significant predictor in dissatisfaction with relief efforts, at least in the case of Pakistan, another argument in favor of independent, population-based surveys of this kind. There is also need to better identify and serve those not residing in camps. Direct surveys of the affected population can be used operationally to assess ongoing needs, more appropriately redirect humanitarian resources, and ultimately, judge the overall quality of a humanitarian response.

Quality of Computationally Inferred Gene Ontology Annotations

PubMed Central

Škunca, Nives; Altenhoff, Adrian; Dessimoz, Christophe

2012-01-01

Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation. PMID:22693439

Qcorp: an annotated classification corpus of Chinese health questions.

PubMed

Guo, Haihong; Na, Xu; Li, Jiao

2018-03-22

Health question-answering (QA) systems have become a typical application scenario of Artificial Intelligent (AI). An annotated question corpus is prerequisite for training machines to understand health information needs of users. Thus, we aimed to develop an annotated classification corpus of Chinese health questions (Qcorp) and make it openly accessible. We developed a two-layered classification schema and corresponding annotation rules on basis of our previous work. Using the schema, we annotated 5000 questions that were randomly selected from 5 Chinese health websites within 6 broad sections. 8 annotators participated in the annotation task, and the inter-annotator agreement was evaluated to ensure the corpus quality. Furthermore, the distribution and relationship of the annotated tags were measured by descriptive statistics and social network map. The questions were annotated using 7101 tags that covers 29 topic categories in the two-layered schema. In our released corpus, the distribution of questions on the top-layered categories was treatment of 64.22%, diagnosis of 37.14%, epidemiology of 14.96%, healthy lifestyle of 10.38%, and health provider choice of 4.54% respectively. Both the annotated health questions and annotation schema were openly accessible on the Qcorp website. Users can download the annotated Chinese questions in CSV, XML, and HTML format. We developed a Chinese health question corpus including 5000 manually annotated questions. It is openly accessible and would contribute to the intelligent health QA system development.

41 CFR 102-74.480 - How many days does a Federal agency have to issue a permit following receipt of a completed...

Code of Federal Regulations, 2010 CFR

2010-07-01

... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false How many days does a Federal agency have to issue a permit following receipt of a completed application? 102-74.480 Section 102... Buildings Permits § 102-74.480 How many days does a Federal agency have to issue a permit following receipt...

Negative Affect and Neural Response to Palatable Food Intake in Bulimia Nervosa

PubMed Central

Bohon, Cara; Stice, Eric

2012-01-01

Binge eating is often preceded by reports of negative affect, but the mechanism by which affect may lead to binge eating is unclear. This study evaluated the effect of negative affect on neural response to anticipation and receipt of palatable food in women with bulimia nervosa (BN) versus healthy controls. We also evaluated connectivity between the amygdala and reward-related brain regions. Females with and without BN (N = 26) underwent functional magnetic resonance imaging (fMRI) during receipt and anticipated receipt of chocolate milkshake and a tasteless solution. We measured negative affect just prior to the scan. Women with BN showed a positive correlation between negative affect and activity in the putamen, caudate, and pallidum during anticipated receipt of milkshake (versus tasteless solution). There were no significant relations between negative affect and receipt of milkshake. Connectivity analyses revealed a greater relation of amygdala activity to activation in the left putamen and insula during anticipated receipt of milkshake in the bulimia group relative to the control group. The opposite pattern was found for the taste of milkshake; the control group showed a greater relation of amygdala activity to activation in the left putamen and insula in response to milkshake receipt than the bulimia group. Results show that as negative affect increases, so does responsivity of reward regions to anticipated intake of palatable food, implying that negative affect may increase the reward value of food for individuals with bulimia nervosa or that negative affect has become a conditioned cue due to a history of binge eating in a negative mood. PMID:22387716

Negative affect and neural response to palatable food intake in bulimia nervosa.

PubMed

Bohon, Cara; Stice, Eric

2012-06-01

Binge eating is often preceded by reports of negative affect, but the mechanism by which affect may lead to binge eating is unclear. This study evaluated the effect of negative affect on neural response to anticipation and receipt of palatable food in women with bulimia nervosa (BN) versus healthy controls. We also evaluated connectivity between the amygdala and reward-related brain regions. Females with and without BN (n=26) underwent functional magnetic resonance imaging (fMRI) during receipt and anticipated receipt of chocolate milkshake and a tasteless solution. We measured negative affect just prior to the scan. Women with BN showed a positive correlation between negative affect and activity in the putamen, caudate, and pallidum during anticipated receipt of milkshake (versus tasteless solution). There were no significant relations between negative affect and receipt of milkshake. Connectivity analyses revealed a greater relation of amygdala activity to activation in the left putamen and insula during anticipated receipt of milkshake in the bulimia group relative to the control group. The opposite pattern was found for the taste of milkshake; the control group showed a greater relation of amygdala activity to activation in the left putamen and insula in response to milkshake receipt than the bulimia group. Results show that as negative affect increases, so does responsivity of reward regions to anticipated intake of palatable food, implying that negative affect may increase the reward value of food for individuals with bulimia nervosa or that negative affect has become a conditioned cue due to a history of binge eating in a negative mood. Copyright © 2012 Elsevier Ltd. All rights reserved.

Subjective health of adolescents from families in receipt of social assistance.

PubMed

Mazur, J; Dzielska, A; Zawadzka, D; Tabak, I; Małkowska-Szkutnik, A

2016-08-01

To compare the subjective health of adolescents from families in receipt and not in receipt of social assistance. Nationwide cross-sectional study of 1812 pupils aged 13-18 years in Poland in 2010-2011. The analysis focused on two dimensions of the Child Health and Illness Profile - Adolescent Edition questionnaire: discomfort and satisfaction with health. Age, sex and seven socio-economic factors were considered as determinants. Overall, 10.8% of the respondents reported that their families were in receipt of social welfare benefits. Among the families of low socio-economic status and living in poor regions, the percentage in receipt of social welfare benefits increased to 22.1%; however, this figure was lower (4.4%) if both parents had a higher level of education. After adjustment for six sociodemographic variables, the standardized regression coefficient of the social welfare benefits variable amounted to 0.072 (P = 0.004) in the discomfort model and -0.044 (P = 0.079) in the satisfaction model. A significant three-level interaction was found (P = 0.007) between residential location, neighbourhood affluence and being in receipt of social welfare benefits as predicators of discomfort score (general linear model). Being in receipt of social welfare benefits has a stronger impact on experiencing discomfort than diminishing satisfaction with one's health. It also has a stronger effect on physical problems than on emotional problems. The item 'on social assistance' is recommended as it helps to identify families particularly exposed to the health consequences of poverty. Copyright © 2015 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

NoGOA: predicting noisy GO annotations using evidences and sparse representation.

PubMed

Yu, Guoxian; Lu, Chang; Wang, Jun

2017-07-21

Gene Ontology (GO) is a community effort to represent functional features of gene products. GO annotations (GOA) provide functional associations between GO terms and gene products. Due to resources limitation, only a small portion of annotations are manually checked by curators, and the others are electronically inferred. Although quality control techniques have been applied to ensure the quality of annotations, the community consistently report that there are still considerable noisy (or incorrect) annotations. Given the wide application of annotations, however, how to identify noisy annotations is an important but yet seldom studied open problem. We introduce a novel approach called NoGOA to predict noisy annotations. NoGOA applies sparse representation on the gene-term association matrix to reduce the impact of noisy annotations, and takes advantage of sparse representation coefficients to measure the semantic similarity between genes. Secondly, it preliminarily predicts noisy annotations of a gene based on aggregated votes from semantic neighborhood genes of that gene. Next, NoGOA estimates the ratio of noisy annotations for each evidence code based on direct annotations in GOA files archived on different periods, and then weights entries of the association matrix via estimated ratios and propagates weights to ancestors of direct annotations using GO hierarchy. Finally, it integrates evidence-weighted association matrix and aggregated votes to predict noisy annotations. Experiments on archived GOA files of six model species (H. sapiens, A. thaliana, S. cerevisiae, G. gallus, B. Taurus and M. musculus) demonstrate that NoGOA achieves significantly better results than other related methods and removing noisy annotations improves the performance of gene function prediction. The comparative study justifies the effectiveness of integrating evidence codes with sparse representation for predicting noisy GO annotations. Codes and datasets are available at http://mlda.swu.edu.cn/codes.php?name=NoGOA .

Annotation Graphs: A Graph-Based Visualization for Meta-Analysis of Data Based on User-Authored Annotations.

PubMed

Zhao, Jian; Glueck, Michael; Breslav, Simon; Chevalier, Fanny; Khan, Azam

2017-01-01

User-authored annotations of data can support analysts in the activity of hypothesis generation and sensemaking, where it is not only critical to document key observations, but also to communicate insights between analysts. We present annotation graphs, a dynamic graph visualization that enables meta-analysis of data based on user-authored annotations. The annotation graph topology encodes annotation semantics, which describe the content of and relations between data selections, comments, and tags. We present a mixed-initiative approach to graph layout that integrates an analyst's manual manipulations with an automatic method based on similarity inferred from the annotation semantics. Various visual graph layout styles reveal different perspectives on the annotation semantics. Annotation graphs are implemented within C8, a system that supports authoring annotations during exploratory analysis of a dataset. We apply principles of Exploratory Sequential Data Analysis (ESDA) in designing C8, and further link these to an existing task typology in the visualization literature. We develop and evaluate the system through an iterative user-centered design process with three experts, situated in the domain of analyzing HCI experiment data. The results suggest that annotation graphs are effective as a method of visually extending user-authored annotations to data meta-analysis for discovery and organization of ideas.

Do Diagnosis Delays Impact Receipt of Test Results? Evidence from the HIV Early Infant Diagnosis Program in Uganda

PubMed Central

Mugambi, Melissa Latigo; Deo, Sarang; Kekitiinwa, Adeodata; Kiyaga, Charles; Singer, Mendel E.

2013-01-01

Background There is scant evidence on the association between diagnosis delays and the receipt of test results in HIV Early Infant Diagnosis (EID) programs. We determine the association between diagnosis delays and other health care system and patient factors on result receipt. Methods We reviewed 703 infant HIV test records for tests performed between January 2008 and February 2009 at a regional referral hospital and level four health center in Uganda. The main outcome was caregiver receipt of the test result. The primary study variable was turnaround time (time between sample collection and result availability at the health facility). Additional variables included clinic entry point, infant age at sample collection, reported HIV status and receipt of antiretroviral prophylaxis for prevention of mother-to-child transmission. We conducted a pooled analysis in addition to separate analyses for each facility. We estimated the relative risk of result receipt using modified Poisson regression with robust standard errors. Results Overall, the median result turnaround time, was 38 days. 59% of caregivers received infant test results. Caregivers were less likely to receive results at turnaround times greater than 49 days compared to 28 days or fewer (ARR = 0.83; 95% CI = 0.70–0.98). Caregivers were more likely to receive results at the PMTCT clinic (ARR = 1.81; 95% CI = 1.40–2.33) and less likely at the pediatric ward (ARR = 0.54; 95% CI = 0.37–0.81) compared to the immunization clinic. At the level four health center, result receipt was half as likely among infants older than 9 months compared to 3 months and younger (ARR= 0.47; 95% CI = 0.25–0.93). Conclusion In this study setting, we find evidence that longer turnaround times, clinic entry point and age at sample collection may be associated with receipt of infant HIV test results. PMID:24282502

An RDF/OWL knowledge base for query answering and decision support in clinical pharmacogenetics.

PubMed

Samwald, Matthias; Freimuth, Robert; Luciano, Joanne S; Lin, Simon; Powers, Robert L; Marshall, M Scott; Adlassnig, Klaus-Peter; Dumontier, Michel; Boyce, Richard D

2013-01-01

Genetic testing for personalizing pharmacotherapy is bound to become an important part of clinical routine. To address associated issues with data management and quality, we are creating a semantic knowledge base for clinical pharmacogenetics. The knowledge base is made up of three components: an expressive ontology formalized in the Web Ontology Language (OWL 2 DL), a Resource Description Framework (RDF) model for capturing detailed results of manual annotation of pharmacogenomic information in drug product labels, and an RDF conversion of relevant biomedical datasets. Our work goes beyond the state of the art in that it makes both automated reasoning as well as query answering as simple as possible, and the reasoning capabilities go beyond the capabilities of previously described ontologies.

45 CFR 286.130 - Does the receipt of Welfare-to-Work (WtW) cash assistance count towards a Tribe's TANF time limit?

Code of Federal Regulations, 2010 CFR

2010-10-01

... 45 Public Welfare 2 2010-10-01 2010-10-01 false Does the receipt of Welfare-to-Work (WtW) cash... and Processing § 286.130 Does the receipt of Welfare-to-Work (WtW) cash assistance count towards a... as well as the penalty provision at § 286.195(a)(1), WtW cash assistance counts towards a Tribe's...

23 CFR 661.43 - Can other sources of funds be used to finance a queued project in advance of receipt of IRRBP funds?

Code of Federal Regulations, 2011 CFR

2011-04-01

... 23 Highways 1 2011-04-01 2011-04-01 false Can other sources of funds be used to finance a queued project in advance of receipt of IRRBP funds? 661.43 Section 661.43 Highways FEDERAL HIGHWAY... PROGRAM § 661.43 Can other sources of funds be used to finance a queued project in advance of receipt of...

23 CFR 661.43 - Can other sources of funds be used to finance a queued project in advance of receipt of IRRBP funds?

Code of Federal Regulations, 2013 CFR

2013-04-01

... 23 Highways 1 2013-04-01 2013-04-01 false Can other sources of funds be used to finance a queued project in advance of receipt of IRRBP funds? 661.43 Section 661.43 Highways FEDERAL HIGHWAY... PROGRAM § 661.43 Can other sources of funds be used to finance a queued project in advance of receipt of...

23 CFR 661.43 - Can other sources of funds be used to finance a queued project in advance of receipt of IRRBP funds?

Code of Federal Regulations, 2014 CFR

2014-04-01

... 23 Highways 1 2014-04-01 2014-04-01 false Can other sources of funds be used to finance a queued project in advance of receipt of IRRBP funds? 661.43 Section 661.43 Highways FEDERAL HIGHWAY... PROGRAM § 661.43 Can other sources of funds be used to finance a queued project in advance of receipt of...

23 CFR 661.43 - Can other sources of funds be used to finance a queued project in advance of receipt of IRRBP funds?

Code of Federal Regulations, 2012 CFR

2012-04-01

... 23 Highways 1 2012-04-01 2012-04-01 false Can other sources of funds be used to finance a queued project in advance of receipt of IRRBP funds? 661.43 Section 661.43 Highways FEDERAL HIGHWAY... PROGRAM § 661.43 Can other sources of funds be used to finance a queued project in advance of receipt of...

Premilitary intimate partner violence and attrition from the U.S. Navy.

PubMed

Merrill, Lex L; Stander, Valerie A; Thomsen, Cynthia J; Crouch, Julie L; Milner, Joel S

2006-12-01

A prospective study of U.S. Navy recruits (N = 5,498) examined whether premilitary intimate partner violence (IPV) was associated with attrition. Overall, more than one-fourth of recruits reported premilitary physical IPV and more than two-thirds reported premilitary verbal IPV. Women reported more perpetration and receipt of IPV than men, and married or cohabiting respondents reported more IPV than single respondents. Both perpetration and receipt of IPV significantly predicted attrition within 4 years. However, after controlling for other forms of IPV, only receipt of physical IPV significantly predicted attrition. In only one analysis did associations between IPV and attrition vary according to marital status or gender; premilitary receipt of verbal IPV had different effects on women and men.

Gene Ontology annotations at SGD: new data sources and annotation methods

PubMed Central

Hong, Eurie L.; Balakrishnan, Rama; Dong, Qing; Christie, Karen R.; Park, Julie; Binkley, Gail; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Krieger, Cynthia J.; Livstone, Michael S.; Miyasato, Stuart R.; Nash, Robert S.; Oughtred, Rose; Skrzypek, Marek S.; Weng, Shuai; Wong, Edith D.; Zhu, Kathy K.; Dolinski, Kara; Botstein, David; Cherry, J. Michael

2008-01-01

The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

DOE PAGES

Brettin, Thomas; Davis, James J.; Disz, Terry; ...

2015-02-10

The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offersmore » a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.« less

Trends in Receipt of Sexually Transmitted Disease Services Among Women 15 to 44 Years Old in the United States, 2002 to 2006–2010

PubMed Central

Haderxhanaj, Laura T.; Gift, Thomas L.; Loosier, Penny S.; Cramer, Ryan C.; Leichliter, Jami S.

2018-01-01

Background To describe recent trends in the receipt of sexually transmitted disease (STD) services among women (age, 15–44 years) from 2002 to 2006–2010 using the National Survey of Family Growth. Methods We analyzed trends in demographics, health insurance, and visit-related variables of women reporting receipt of STD services (counseling, testing, or treatment) in the past 12 months. We also analyzed trends in the source of STD services and the payment method used. Results Receipt of STD services reported by women in the past 12 months increased from 2002 (12.6%) to 2006–2010 (16.0%; P < 0.001). Receipt of services did not increase among adolescents (P = 0.592). Among women receiving STD services from a private doctor/HMO, the percentage with private insurance decreased over time (74.6%–66.8%), whereas the percentage with Medicaid increased (12.8%–19.7%; P = 0.020). For women receiving STD services at a public clinic or nonprimary care facility, there were no statistically significant differences by demographics, except that fewer adolescents but more young adults reported using a public clinic over time (P = 0.038). Among women who reported using Medicaid as payment, receipt of STD services at a public clinic significantly decreased (36.8%–25.4%; P = 0.019). For women who paid for STD services with private insurance, the only significant difference was an increase in having a copay over time (61.3%–70.1%; P = 0.012). Conclusions Despite a significant increase in receipt of STD services over time, many women at risk for STDs did not receive services including adolescents. In addition, we identified important shifts in payment methods during this time frame. PMID:24335746

Receipt of Preventive Services After Oregon's Randomized Medicaid Experiment.

PubMed

Marino, Miguel; Bailey, Steffani R; Gold, Rachel; Hoopes, Megan J; O'Malley, Jean P; Huguet, Nathalie; Heintzman, John; Gallia, Charles; McConnell, K John; DeVoe, Jennifer E

2016-02-01

It is predicted that gaining health insurance via the Affordable Care Act will result in increased rates of preventive health services receipt in the U.S., primarily based on self-reported findings from previous health insurance expansion studies. This study examined the long-term (36-month) impact of Oregon's 2008 randomized Medicaid expansion ("Oregon Experiment") on receipt of 12 preventive care services in community health centers using electronic health record data. Demographic data from adult (aged 19-64 years) Oregon Experiment participants were probabilistically matched to electronic health record data from 49 Oregon community health centers within the OCHIN community health information network (N=10,643). Intent-to-treat analyses compared receipt of preventive services over a 36-month (2008-2011) period among those randomly assigned to apply for Medicaid versus not assigned, and instrumental variable analyses estimated the effect of actually gaining Medicaid coverage on preventive services receipt (data collected in 2012-2014; analysis performed in 2014-2015). Intent-to-treat analyses revealed statistically significant differences between patients randomly assigned to apply for Medicaid (versus not assigned) for 8 of 12 assessed preventive services. In intent-to-treat analyses, Medicaid coverage significantly increased the odds of receipt of most preventive services (ORs ranging from 1.04 [95% CI=1.02, 1.06] for smoking assessment to 1.27 [95% CI=1.02, 1.57] for mammography). Rates of preventive services receipt will likely increase as community health center patients gain insurance through Affordable Care Act expansions. Continued effort is needed to increase health insurance coverage in an effort to decrease health disparities in vulnerable populations. Copyright © 2016 American Journal of Preventive Medicine. Published by Elsevier Inc. All rights reserved.

Receipt of Preventive Services After Oregon’s Randomized Medicaid Experiment

PubMed Central

Marino, Miguel; Bailey, Steffani R.; Gold, Rachel; Hoopes, Megan J.; O’Malley, Jean P.; Huguet, Nathalie; Heintzman, John; Gallia, Charles; McConnell, K. John; DeVoe, Jennifer E.

2015-01-01

Introduction It is predicted that gaining health insurance via the Affordable Care Act will result in increased rates of preventive health services receipt in the U.S, primarily based on self-reported findings from previous health insurance expansion studies. This study examined the long-term (36-month) impact of Oregon’s 2008 randomized Medicaid expansion (“Oregon Experiment”) on receipt of 12 preventive care services in community health centers using electronic health record data. Methods Demographic data from adult (aged 19–64 years) Oregon Experiment participants were probabilistically matched to electronic health record data from 49 Oregon community health centers within the OCHIN community health information network (N=10,643). Intent-to-treat analyses compared receipt of preventive services over a 36-month (2008–2011) period among those randomly assigned to apply for Medicaid versus not assigned, and instrumental variable analyses estimated the effect of actually gaining Medicaid coverage on preventive services receipt (data collected in 2012–2014; analysis performed in 2014–2015). Results Intent-to-treat analyses revealed statistically significant differences between patients randomly assigned to apply for Medicaid (versus not assigned) for eight of 12 assessed preventive services. In intent-to-treat[MM1] analyses, Medicaid coverage significantly increased the odds of receipt of most preventive services (ORs ranging from 1.04 [95% CI=1.02, 1.06] for smoking assessment to 1.27 [95% CI=1.02, 1.57] for mammography). Conclusions Rates of preventive services receipt will likely increase as community health center patients gain insurance through Affordable Care Act expansions. Continued effort is needed to increase health insurance coverage in an effort to decrease health disparities in vulnerable populations. PMID:26497264

Radiologist income, receipts, and academic performance: an analysis of many nations.

PubMed

Semelka, Richard C; Busireddy, K K; Burke, Lauren Mb; Ramalho, Miguel; Martí-Bonmatí, Luis; Morana, Giovanni; AlObaidy, Mamdoh; Elias, Jorge

2016-12-01

Background Considerable interest exists in comparison between healthcare systems across multiple countries, especially where cost enters the discussion. Purpose To evaluate the relationship between radiologists' income, receipts for studies, and academic performance across multiple countries. Material and Methods The annual income of radiologists and receipts for computed tomography (CT) and magnetic resonance imaging (MRI) were obtained based on a survey sent to expert radiologists practicing in 23 countries of varying developmental status. Articles published in generalist radiology journals determined the academic performance of each country. Results Among the developed countries, Canada has the highest estimated annual income for both private ($700,000/year) and university radiologists ($600,000/year) while Spain has the lowest income for private practice ($68,000/year) and Portugal has the lowest income for university practice ($57,300/year). Among the developing countries, Saudi Arabia has the highest incomes for both private ($210,000/year) and university ($140,000/year) radiologists and Vietnam has the lowest incomes for both private ($30,000/year) and university ($6,000/year) radiologists. Total receipts for CT and MRI studies ranged from $80/study (Portugal) to $1000/study (USA) in developed countries, and ranged from $30/study (Egypt) to $700/study (Saudi Arabia) in developing countries. A moderate correlation ( r = 0.482) was seen between radiologist's income and the receipts for combined practice in all countries. The radiology journal academic quotient was highest in The Netherlands among developed countries, and Turkey among developing countries. Conclusion A relatively broad range of radiologists' income is observed among developed and developing countries, which shows correlation with the receipts for advanced imaging studies. Countries with an acceptable compromise between income, receipts, and academic performance, may be the best models for other countries to emulate.

One and done? Equality of opportunity and repeated access to scarce, indivisible medical resources

PubMed Central

2012-01-01

Background Existing ethical guidelines recommend that, all else equal, past receipt of a medical resource (e.g. a scarce organ) should not be considered in current allocation decisions (e.g. a repeat transplantation). Discussion One stated reason for this ethical consensus is that formal theories of ethics and justice do not persuasively accept or reject repeated access to the same medical resources. Another is that restricting attention to past receipt of a particular medical resource seems arbitrary: why couldn’t one just as well, it is argued, consider receipt of other goods such as income or education? In consequence, simple allocation by lottery or first-come-first-served without consideration of any past receipt is thought to best afford equal opportunity, conditional on equal medical need. There are three issues with this view that need to be addressed. First, public views and patient preferences are less ambiguous than formal theories of ethics. Empirical work shows strong preferences for fairness in health care that have not been taken into account: repeated access to resources has been perceived as unfair. Second, while difficult to consider receipt of many other prior resources including non-medical resources, this should not be used a motive for ignoring the receipt of any and all goods including the focal resource in question. Third, when all claimants to a scarce resource are equally deserving, then use of random allocation seems warranted. However, the converse is not true: mere use of a randomizer does not by itself make the merits of all claimants equal. Summary My conclusion is that not ignoring prior receipt of the same medical resource, and prioritizing those who have not previously had access to the medical resource in question, may be perceived as fairer and more equitable by society. PMID:22624597

One and done? Equality of opportunity and repeated access to scarce, indivisible medical resources.

PubMed

Huesch, Marco D

2012-05-24

Existing ethical guidelines recommend that, all else equal, past receipt of a medical resource (e.g. a scarce organ) should not be considered in current allocation decisions (e.g. a repeat transplantation). One stated reason for this ethical consensus is that formal theories of ethics and justice do not persuasively accept or reject repeated access to the same medical resources. Another is that restricting attention to past receipt of a particular medical resource seems arbitrary: why couldn't one just as well, it is argued, consider receipt of other goods such as income or education? In consequence, simple allocation by lottery or first-come-first-served without consideration of any past receipt is thought to best afford equal opportunity, conditional on equal medical need.There are three issues with this view that need to be addressed. First, public views and patient preferences are less ambiguous than formal theories of ethics. Empirical work shows strong preferences for fairness in health care that have not been taken into account: repeated access to resources has been perceived as unfair. Second, while difficult to consider receipt of many other prior resources including non-medical resources, this should not be used a motive for ignoring the receipt of any and all goods including the focal resource in question. Third, when all claimants to a scarce resource are equally deserving, then use of random allocation seems warranted. However, the converse is not true: mere use of a randomizer does not by itself make the merits of all claimants equal. My conclusion is that not ignoring prior receipt of the same medical resource, and prioritizing those who have not previously had access to the medical resource in question, may be perceived as fairer and more equitable by society.

Variation in Educational Services Receipt Among US Children with Developmental Conditions

PubMed Central

Lindly, Olivia J.; Sinche, Brianna K.; Zuckerman, Katharine E.

2015-01-01

Objectives This study examined (1) the relationship between ease of access to needed community-based services (ease of access) and educational services receipt and (2) variation in educational services receipt by sociodemographic and need factors among a nationally representative sample of children with autism spectrum disorder (ASD), developmental delay (DD), and/or intellectual disability (ID). Methods Data from the 2009–10 National Survey of Children with Special Health Care Needs were linked to the 2011 Survey of Pathways to Diagnosis and Services on a sample of 3,502 US children aged 6–17 years with ASD, DD, and/or ID. Descriptive statistics, chi-square tests, and multivariable logistic regression models were used to determine associations of educational services receipt with (1) ease of access and (2) sociodemographic and need factors. Results Among children with developmental conditions, nearly half (49.7%) lacked easy access to services and 16.9% did not have an individualized education program (IEP). Among children with an IEP, those with ease of access were more likely to have an IEP that addressed parent concerns about the child’s development and education than those unable to easily access services (aOR: 2.77; 95% CI: 1.71–4.49). Need factors, including functional limitations status, care coordination need, developmental condition type, and early intervention receipt, were significantly associated with educational services receipt. Conclusions Cross-systems initiatives facilitating service access remain important to ensuring the developmental needs of children with ASD, DD, and/or ID are met. Increased inter-professional collaboration promoting quality educational services receipt for children diagnosed with developmental conditions may further reduce disparities. PMID:26344719

Variation in Educational Services Receipt Among US Children With Developmental Conditions.

PubMed

Lindly, Olivia J; Sinche, Brianna K; Zuckerman, Katharine E

2015-01-01

To examine the relationship between ease of access to needed community-based services (ease of access) and educational services receipt, and variation in educational services receipt by sociodemographic and need factors among a nationally representative sample of children with autism spectrum disorder (ASD), developmental delay (DD), and/or intellectual disability (ID). Data from the 2009-2010 National Survey of Children with Special Health Care Needs were linked to the 2011 Survey of Pathways to Diagnosis and Services on a sample of 3502 US children aged 6 to 17 years with ASD, DD, and/or ID. Descriptive statistics, chi-square tests, and multivariable logistic regression models were used to determine associations of educational services receipt with ease of access and sociodemographic and need factors. Among children with developmental conditions, nearly half (49.7%) lacked easy access to services, and 16.9% did not have an individualized education program (IEP). Among children with an IEP, those with ease of access were more likely to have an IEP that addressed parent concerns about the child's development and education than those unable to easily access services (adjusted odds ratio 2.77; 95% confidence interval 1.71-4.49). Need factors, including functional limitations status, care coordination need, developmental condition type, and early intervention receipt, were significantly associated with educational services receipt. Cross-systems initiatives facilitating service access remain important to ensuring the developmental needs of children with ASD, DD, and/or ID are met. Increased interprofessional collaboration promoting quality educational services receipt for children diagnosed with developmental conditions may further reduce disparities. Copyright © 2015 Academic Pediatric Association. Published by Elsevier Inc. All rights reserved.

An Annotated and Federated Digital Library of Marine Animal Sounds

DTIC Science & Technology

2005-01-01

of the annotations and the relevant segment delimitation points and linkages to other relevant metadata fields; e) search engines that support the...annotators to add information to the same recording, and search engines that permit either all-annotator or specific-annotator searches. To our knowledge

Changes in Adolescents’ Receipt of Sex Education, 2006–2013

PubMed Central

Lindberg, Laura Duberstein; Maddow-Zimet, Isaac; Boonstra, Heather

2016-01-01

Purpose Updated estimates of adolescents’ receipt of sex education are needed to monitor changing access to information. Methods Using nationally representative data from the 2006–2010 and 2011–2013 National Survey of Family Growth, we estimated changes over time in adolescents’ receipt of sex education from formal sources and from parents and differentials in these trends by adolescents’ gender, race/ethnicity, age, and place of residence. Results Between 2006–2010 and 2011–2013, there were significant declines in adolescent females’ receipt of formal instruction about birth control (70% to 60%), saying no to sex (89% to 82%), sexually transmitted disease (94% to 90%), and HIV/AIDS (89% to 86%). There was a significant decline in males’ receipt of instruction about birth control (61% to 55%). Declines were concentrated among adolescents living in nonmetropolitan areas. The proportion of adolescents talking with their parents about sex education topics did not change significantly. Twenty-one percent of females and 35% of males did not receive instruction about methods of birth control from either formal sources or a parent. Conclusions Declines in receipt of formal sex education and low rates of parental communication may leave adolescents without instruction, particularly in nonmetropolitan areas. More effort is needed to understand this decline and to explore adolescents’ potential other sources of reproductive health information. PMID:27032487

Receipt of Pharmacotherapy for Opioid Use Disorder by Justice-Involved U.S. Veterans Health Administration Patients

PubMed Central

Finlay, Andrea K.; Harris, Alex H.S.; Rosenthal, Joel; Blue-Howells, Jessica; Clark, Sean; McGuire, Jim; Timko, Christine; Frayne, Susan M.; Smelson, David; Oliva, Elizabeth; Binswanger, Ingrid

2016-01-01

Background Pharmacotherapy – methadone, buprenorphine, or naltrexone – is an evidence-based treatment for opioid use disorder, but little is known about receipt of these medications among veterans involved in the justice system. The current study examines receipt of pharmacotherapy for opioid use disorder among veterans with a history of justice involvement at U.S. Veterans Health Administration (VHA) facilities compared to veterans with no justice involvement. Methods Using national VHA clinical and pharmacy records, we conducted a retrospective cohort study of veterans with an opioid use disorder diagnosis in fiscal year 2012. Using a mixed-effects logistic regression model, we examined receipt of pharmacotherapy in the 1-year period following diagnosis as a function of justice involvement, adjusting for patient and facility characteristics. Results The 1-year rate of receipt for pharmacotherapy for opioid use disorder was 27% for prison-involved veterans, 34% for jail/court-involved veterans, and 33% for veterans not justice-involved. Compared to veterans not justice-involved, those prison-involved had 0.75 lower adjusted odds (95% confidence interval [CI]: 0.65–0.87) of receiving pharmacotherapy whereas jail/court-involved veterans did not have significantly different adjusted odds. Conclusions Targeted efforts to increase receipt of pharmacotherapy for opioid use disorder among veterans exiting prison is needed as they have lower odds of receiving these medications. PMID:26832998

Caloric Deprivation Increases Responsivity of Attention and Reward Brain Regions to Intake, Anticipated Intake, and Images of Palatable Foods

PubMed Central

Stice, Eric; Burger, Kyle; Yokum, Sonja

2013-01-01

Dietary restraint theoretically increases risk for binge eating, but prospective and experimental studies have produced contradictory findings, apparently because dietary restraint scales do not identify individuals who are reducing caloric intake. Yet, experimentally manipulated caloric deprivation increases responsivity of brain regions implicated in attention and reward to food images, which may contribute to binge eating. We tested whether self-imposed acute and longer-term caloric restriction increases responsivity of attention and reward regions to images, anticipated receipt, and receipt of palatable food using functional magnetic resonance imaging among female and male adolescents (Study 1 N = 34; Study 2 N = 51/81). Duration of acute caloric deprivation correlated positively with activation in regions implicated in attention, reward, and motivation in response to images, anticipated receipt, and receipt of palatable food (e.g., anterior cingulate cortex, orbitofrontal cortex, putamen, and precentral gyrus respectively). Youth in a longer-term negative energy balance likewise showed greater activation in attention (anterior cingulate cortex, ventral medial prefrontal cortex), visual processing (superior visual cortex), reward (caudate) and memory (hippocampus) regions in response to receipt and anticipated receipt of palatable food relative to those in neutral or positive energy balance. Results confirm that self-imposed caloric deprivation increases responsivity of attention, reward, and motivation regions to food, which may explain why caloric deprivation weight loss diets typically do not produce lasting weight loss. PMID:23201365

Prokaryotic Contig Annotation Pipeline Server: Web Application for a Prokaryotic Genome Annotation Pipeline Based on the Shiny App Package.

PubMed

Park, Byeonghyeok; Baek, Min-Jeong; Min, Byoungnam; Choi, In-Geol

2017-09-01

Genome annotation is a primary step in genomic research. To establish a light and portable prokaryotic genome annotation pipeline for use in individual laboratories, we developed a Shiny app package designated as "P-CAPS" (Prokaryotic Contig Annotation Pipeline Server). The package is composed of R and Python scripts that integrate publicly available annotation programs into a server application. P-CAPS is not only a browser-based interactive application but also a distributable Shiny app package that can be installed on any personal computer. The final annotation is provided in various standard formats and is summarized in an R markdown document. Annotation can be visualized and examined with a public genome browser. A benchmark test showed that the annotation quality and completeness of P-CAPS were reliable and compatible with those of currently available public pipelines.

Computer systems for annotation of single molecule fragments

DOEpatents

Schwartz, David Charles; Severin, Jessica

2016-07-19

There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

A guide to best practices for Gene Ontology (GO) manual annotation

PubMed Central

Balakrishnan, Rama; Harris, Midori A.; Huntley, Rachael; Van Auken, Kimberly; Cherry, J. Michael

2013-01-01

The Gene Ontology Consortium (GOC) is a community-based bioinformatics project that classifies gene product function through the use of structured controlled vocabularies. A fundamental application of the Gene Ontology (GO) is in the creation of gene product annotations, evidence-based associations between GO definitions and experimental or sequence-based analysis. Currently, the GOC disseminates 126 million annotations covering >374 000 species including all the kingdoms of life. This number includes two classes of GO annotations: those created manually by experienced biocurators reviewing the literature or by examination of biological data (1.1 million annotations covering 2226 species) and those generated computationally via automated methods. As manual annotations are often used to propagate functional predictions between related proteins within and between genomes, it is critical to provide accurate consistent manual annotations. Toward this goal, we present here the conventions defined by the GOC for the creation of manual annotation. This guide represents the best practices for manual annotation as established by the GOC project over the past 12 years. We hope this guide will encourage research communities to annotate gene products of their interest to enhance the corpus of GO annotations available to all. Database URL: http://www.geneontology.org PMID:23842463

GARNET--gene set analysis with exploration of annotation relations.

PubMed

Rho, Kyoohyoung; Kim, Bumjin; Jang, Youngjun; Lee, Sanghyun; Bae, Taejeong; Seo, Jihae; Seo, Chaehwa; Lee, Jihyun; Kang, Hyunjung; Yu, Ungsik; Kim, Sunghoon; Lee, Sanghyuk; Kim, Wan Kyu

2011-02-15

Gene set analysis is a powerful method of deducing biological meaning for an a priori defined set of genes. Numerous tools have been developed to test statistical enrichment or depletion in specific pathways or gene ontology (GO) terms. Major difficulties towards biological interpretation are integrating diverse types of annotation categories and exploring the relationships between annotation terms of similar information. GARNET (Gene Annotation Relationship NEtwork Tools) is an integrative platform for gene set analysis with many novel features. It includes tools for retrieval of genes from annotation database, statistical analysis & visualization of annotation relationships, and managing gene sets. In an effort to allow access to a full spectrum of amassed biological knowledge, we have integrated a variety of annotation data that include the GO, domain, disease, drug, chromosomal location, and custom-defined annotations. Diverse types of molecular networks (pathways, transcription and microRNA regulations, protein-protein interaction) are also included. The pair-wise relationship between annotation gene sets was calculated using kappa statistics. GARNET consists of three modules--gene set manager, gene set analysis and gene set retrieval, which are tightly integrated to provide virtually automatic analysis for gene sets. A dedicated viewer for annotation network has been developed to facilitate exploration of the related annotations. GARNET (gene annotation relationship network tools) is an integrative platform for diverse types of gene set analysis, where complex relationships among gene annotations can be easily explored with an intuitive network visualization tool (http://garnet.isysbio.org/ or http://ercsb.ewha.ac.kr/garnet/).

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

Buttler, D J

The Java Metadata Facility is introduced by Java Specification Request (JSR) 175 [1], and incorporated into the Java language specification [2] in version 1.5 of the language. The specification allows annotations on Java program elements: classes, interfaces, methods, and fields. Annotations give programmers a uniform way to add metadata to program elements that can be used by code checkers, code generators, or other compile-time or runtime components. Annotations are defined by annotation types. These are defined the same way as interfaces, but with the symbol {at} preceding the interface keyword. There are additional restrictions on defining annotation types: (1) Theymore » cannot be generic; (2) They cannot extend other annotation types or interfaces; (3) Methods cannot have any parameters; (4) Methods cannot have type parameters; (5) Methods cannot throw exceptions; and (6) The return type of methods of an annotation type must be a primitive, a String, a Class, an annotation type, or an array, where the type of the array is restricted to one of the four allowed types. See [2] for additional restrictions and syntax. The methods of an annotation type define the elements that may be used to parameterize the annotation in code. Annotation types may have default values for any of its elements. For example, an annotation that specifies a defect report could initialize an element defining the defect outcome submitted. Annotations may also have zero elements. This could be used to indicate serializability for a class (as opposed to the current Serializability interface).« less

8 CFR 244.9 - Evidence.

Code of Federal Regulations, 2013 CFR

2013-01-01

... company. (ii) Rent receipts, utility bills (gas, electric, telephone, etc.), receipts, or letters from... United States showing name of school and period(s) of school attendance; (iv) Hospital or medical records...

8 CFR 244.9 - Evidence.

Code of Federal Regulations, 2012 CFR

2012-01-01

... company. (ii) Rent receipts, utility bills (gas, electric, telephone, etc.), receipts, or letters from... United States showing name of school and period(s) of school attendance; (iv) Hospital or medical records...

8 CFR 244.9 - Evidence.

Code of Federal Regulations, 2011 CFR

2011-01-01

... company. (ii) Rent receipts, utility bills (gas, electric, telephone, etc.), receipts, or letters from... United States showing name of school and period(s) of school attendance; (iv) Hospital or medical records...

8 CFR 244.9 - Evidence.

Code of Federal Regulations, 2014 CFR

2014-01-01

... company. (ii) Rent receipts, utility bills (gas, electric, telephone, etc.), receipts, or letters from... United States showing name of school and period(s) of school attendance; (iv) Hospital or medical records...

Punishment and Welfare: Paternal Incarceration and Families' Receipt of Public Assistance.

PubMed

Sugie, Naomi F

2012-01-01

The United States criminal justice and welfare systems are two important government institutions in the lives of the poor. Despite many theoretical discussions about their relationship, their operation at the level of offenders and families remains poorly understood. This paper utilizes Fragile Families and Child Wellbeing data to examine how recent paternal incarceration is associated with families' receipt of TANF, food stamps, and Medicaid/SCHIP. Results robust to multiple tests find that incarceration is not related to subsequent TANF receipt but is significantly associated with increased receipt of food stamps and Medicaid/SCHIP. The findings suggest that greater government involvement among poor families is an unexpected consequence of mass imprisonment; however, increased participation does not include TANF-the cash assistance program of most concern to theorists.

Whole exome sequencing is an efficient, sensitive and specific method of mutation detection in osteogenesis imperfecta and Marfan syndrome

PubMed Central

McInerney-Leo, Aideen M; Marshall, Mhairi S; Gardiner, Brooke; Coucke, Paul J; Van Laer, Lut; Loeys, Bart L; Summers, Kim M; Symoens, Sofie; West, Jennifer A; West, Malcolm J; Paul Wordsworth, B; Zankl, Andreas; Leo, Paul J; Brown, Matthew A; Duncan, Emma L

2013-01-01

Osteogenesis imperfecta (OI) and Marfan syndrome (MFS) are common Mendelian disorders. Both conditions are usually diagnosed clinically, as genetic testing is expensive due to the size and number of potentially causative genes and mutations. However, genetic testing may benefit patients, at-risk family members and individuals with borderline phenotypes, as well as improving genetic counseling and allowing critical differential diagnoses. We assessed whether whole exome sequencing (WES) is a sensitive method for mutation detection in OI and MFS. WES was performed on genomic DNA from 13 participants with OI and 10 participants with MFS who had known mutations, with exome capture followed by massive parallel sequencing of multiplexed samples. Single nucleotide polymorphisms (SNPs) and small indels were called using Genome Analysis Toolkit (GATK) and annotated with ANNOVAR. CREST, exomeCopy and exomeDepth were used for large deletion detection. Results were compared with the previous data. Specificity was calculated by screening WES data from a control population of 487 individuals for mutations in COL1A1, COL1A2 and FBN1. The target capture of five exome capture platforms was compared. All 13 mutations in the OI cohort and 9/10 in the MFS cohort were detected (sensitivity=95.6%) including non-synonymous SNPs, small indels (<10 bp), and a large UTR5/exon 1 deletion. One mutation was not detected by GATK due to strand bias. Specificity was 99.5%. Capture platforms and analysis programs differed considerably in their ability to detect mutations. Consumable costs for WES were low. WES is an efficient, sensitive, specific and cost-effective method for mutation detection in patients with OI and MFS. Careful selection of platform and analysis programs is necessary to maximize success. PMID:24501682

Large-scale inference of gene function through phylogenetic annotation of Gene Ontology terms: case study of the apoptosis and autophagy cellular processes.

PubMed

Feuermann, Marc; Gaudet, Pascale; Mi, Huaiyu; Lewis, Suzanna E; Thomas, Paul D

2016-01-01

We previously reported a paradigm for large-scale phylogenomic analysis of gene families that takes advantage of the large corpus of experimentally supported Gene Ontology (GO) annotations. This 'GO Phylogenetic Annotation' approach integrates GO annotations from evolutionarily related genes across ∼100 different organisms in the context of a gene family tree, in which curators build an explicit model of the evolution of gene functions. GO Phylogenetic Annotation models the gain and loss of functions in a gene family tree, which is used to infer the functions of uncharacterized (or incompletely characterized) gene products, even for human proteins that are relatively well studied. Here, we report our results from applying this paradigm to two well-characterized cellular processes, apoptosis and autophagy. This revealed several important observations with respect to GO annotations and how they can be used for function inference. Notably, we applied only a small fraction of the experimentally supported GO annotations to infer function in other family members. The majority of other annotations describe indirect effects, phenotypes or results from high throughput experiments. In addition, we show here how feedback from phylogenetic annotation leads to significant improvements in the PANTHER trees, the GO annotations and GO itself. Thus GO phylogenetic annotation both increases the quantity and improves the accuracy of the GO annotations provided to the research community. We expect these phylogenetically based annotations to be of broad use in gene enrichment analysis as well as other applications of GO annotations.Database URL: http://amigo.geneontology.org/amigo. © The Author(s) 2016. Published by Oxford University Press.

AnnotateGenomicRegions: a web application.

PubMed

Zammataro, Luca; DeMolfetta, Rita; Bucci, Gabriele; Ceol, Arnaud; Muller, Heiko

2014-01-01

Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user. The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions.

AnnotateGenomicRegions: a web application

PubMed Central

2014-01-01

Background Modern genomic technologies produce large amounts of data that can be mapped to specific regions in the genome. Among the first steps in interpreting the results is annotation of genomic regions with known features such as genes, promoters, CpG islands etc. Several tools have been published to perform this task. However, using these tools often requires a significant amount of bioinformatics skills and/or downloading and installing dedicated software. Results Here we present AnnotateGenomicRegions, a web application that accepts genomic regions as input and outputs a selection of overlapping and/or neighboring genome annotations. Supported organisms include human (hg18, hg19), mouse (mm8, mm9, mm10), zebrafish (danRer7), and Saccharomyces cerevisiae (sacCer2, sacCer3). AnnotateGenomicRegions is accessible online on a public server or can be installed locally. Some frequently used annotations and genomes are embedded in the application while custom annotations may be added by the user. Conclusions The increasing spread of genomic technologies generates the need for a simple-to-use annotation tool for genomic regions that can be used by biologists and bioinformaticians alike. AnnotateGenomicRegions meets this demand. AnnotateGenomicRegions is an open-source web application that can be installed on any personal computer or institute server. AnnotateGenomicRegions is available at: http://cru.genomics.iit.it/AnnotateGenomicRegions. PMID:24564446

Evaluation of web-based annotation of ophthalmic images for multicentric clinical trials.

PubMed

Chalam, K V; Jain, P; Shah, V A; Shah, Gaurav Y

2006-06-01

An Internet browser-based annotation system can be used to identify and describe features in digitalized retinal images, in multicentric clinical trials, in real time. In this web-based annotation system, the user employs a mouse to draw and create annotations on a transparent layer, that encapsulates the observations and interpretations of a specific image. Multiple annotation layers may be overlaid on a single image. These layers may correspond to annotations by different users on the same image or annotations of a temporal sequence of images of a disease process, over a period of time. In addition, geometrical properties of annotated figures may be computed and measured. The annotations are stored in a central repository database on a server, which can be retrieved by multiple users in real time. This system facilitates objective evaluation of digital images and comparison of double-blind readings of digital photographs, with an identifiable audit trail. Annotation of ophthalmic images allowed clinically feasible and useful interpretation to track properties of an area of fundus pathology. This provided an objective method to monitor properties of pathologies over time, an essential component of multicentric clinical trials. The annotation system also allowed users to view stereoscopic images that are stereo pairs. This web-based annotation system is useful and valuable in monitoring patient care, in multicentric clinical trials, telemedicine, teaching and routine clinical settings.

Evaluating Hierarchical Structure in Music Annotations

PubMed Central

McFee, Brian; Nieto, Oriol; Farbood, Morwaread M.; Bello, Juan Pablo

2017-01-01

Music exhibits structure at multiple scales, ranging from motifs to large-scale functional components. When inferring the structure of a piece, different listeners may attend to different temporal scales, which can result in disagreements when they describe the same piece. In the field of music informatics research (MIR), it is common to use corpora annotated with structural boundaries at different levels. By quantifying disagreements between multiple annotators, previous research has yielded several insights relevant to the study of music cognition. First, annotators tend to agree when structural boundaries are ambiguous. Second, this ambiguity seems to depend on musical features, time scale, and genre. Furthermore, it is possible to tune current annotation evaluation metrics to better align with these perceptual differences. However, previous work has not directly analyzed the effects of hierarchical structure because the existing methods for comparing structural annotations are designed for “flat” descriptions, and do not readily generalize to hierarchical annotations. In this paper, we extend and generalize previous work on the evaluation of hierarchical descriptions of musical structure. We derive an evaluation metric which can compare hierarchical annotations holistically across multiple levels. sing this metric, we investigate inter-annotator agreement on the multilevel annotations of two different music corpora, investigate the influence of acoustic properties on hierarchical annotations, and evaluate existing hierarchical segmentation algorithms against the distribution of inter-annotator agreement. PMID:28824514

8 CFR 1244.9 - Evidence.

Code of Federal Regulations, 2014 CFR

2014-01-01

...) Duties with the company. (ii) Rent receipts, utility bills (gas, electric, telephone, etc.), receipts, or... the United States showing name of school and period(s) of school attendance; (iv) Hospital or medical...

8 CFR 1244.9 - Evidence.

Code of Federal Regulations, 2011 CFR

2011-01-01

...) Duties with the company. (ii) Rent receipts, utility bills (gas, electric, telephone, etc.), receipts, or... the United States showing name of school and period(s) of school attendance; (iv) Hospital or medical...

8 CFR 1244.9 - Evidence.

Code of Federal Regulations, 2013 CFR

2013-01-01

...) Duties with the company. (ii) Rent receipts, utility bills (gas, electric, telephone, etc.), receipts, or... the United States showing name of school and period(s) of school attendance; (iv) Hospital or medical...

8 CFR 1244.9 - Evidence.

Code of Federal Regulations, 2012 CFR

2012-01-01

...) Duties with the company. (ii) Rent receipts, utility bills (gas, electric, telephone, etc.), receipts, or... the United States showing name of school and period(s) of school attendance; (iv) Hospital or medical...

Annotations and the Collaborative Digital Library: Effects of an Aligned Annotation Interface on Student Argumentation and Reading Strategies

ERIC Educational Resources Information Center

Wolfe, Joanna

2008-01-01

Recent research on annotation interfaces provides provocative evidence that anchored, annotation-based discussion environments may lead to better conversations about a text. However, annotation interfaces raise complicated tradeoffs regarding screen real estate and positioning. It is argued that solving this screen real estate problem requires…

IMG ER: a system for microbial genome annotation expert review and curation.

PubMed

Markowitz, Victor M; Mavromatis, Konstantinos; Ivanova, Natalia N; Chen, I-Min A; Chu, Ken; Kyrpides, Nikos C

2009-09-01

A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

HAMAP in 2013, new developments in the protein family classification and annotation system

PubMed Central

Pedruzzi, Ivo; Rivoire, Catherine; Auchincloss, Andrea H.; Coudert, Elisabeth; Keller, Guillaume; de Castro, Edouard; Baratin, Delphine; Cuche, Béatrice A.; Bougueleret, Lydie; Poux, Sylvain; Redaschi, Nicole; Xenarios, Ioannis; Bridge, Alan

2013-01-01

HAMAP (High-quality Automated and Manual Annotation of Proteins—available at http://hamap.expasy.org/) is a system for the classification and annotation of protein sequences. It consists of a collection of manually curated family profiles for protein classification, and associated annotation rules that specify annotations that apply to family members. HAMAP was originally developed to support the manual curation of UniProtKB/Swiss-Prot records describing microbial proteins. Here we describe new developments in HAMAP, including the extension of HAMAP to eukaryotic proteins, the use of HAMAP in the automated annotation of UniProtKB/TrEMBL, providing high-quality annotation for millions of protein sequences, and the future integration of HAMAP into a unified system for UniProtKB annotation, UniRule. HAMAP is continuously updated by expert curators with new family profiles and annotation rules as new protein families are characterized. The collection of HAMAP family classification profiles and annotation rules can be browsed and viewed on the HAMAP website, which also provides an interface to scan user sequences against HAMAP profiles. PMID:23193261

Navy Controls for Invoice, Receipt, Acceptance, and Property Transfer System Need Improvement

DTIC Science & Technology

2016-02-25

iR APT as a web-based system to electronically invoice, receipt, and accept ser vices and product s from its contractors and vendors. The iR APT system...electronically shares document s bet ween DoD and it s contractors and vendors to eliminate redundant data entr y, increase data accuracy, and reduce...The iR APT system allows contractors to submit and track invoices and receipt and acceptance documents over the web and allows government personnel to

7 CFR 1485.20 - Financial management, reports, evaluations and appeals.

Code of Federal Regulations, 2010 CFR

2010-01-01

...) COMMODITY CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS COOPERATIVE...) Receipts for all STRE (actual vendor invoices or restaurant checks, rather than credit card receipts); (ii...

48 CFR 15.606-1 - Receipt and initial review.

Code of Federal Regulations, 2010 CFR

2010-10-01

... CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Unsolicited Proposals 15.606-1 Receipt and... information for evaluation; (5) Has overall scientific, technical, or socioeconomic merit; (6) Has been...

48 CFR 15.606-1 - Receipt and initial review.

Code of Federal Regulations, 2011 CFR

2011-10-01

... CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Unsolicited Proposals 15.606-1 Receipt and... information for evaluation; (5) Has overall scientific, technical, or socioeconomic merit; (6) Has been...

48 CFR 15.606-1 - Receipt and initial review.

Code of Federal Regulations, 2012 CFR

2012-10-01

... CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Unsolicited Proposals 15.606-1 Receipt and... information for evaluation; (5) Has overall scientific, technical, or socioeconomic merit; (6) Has been...

48 CFR 15.606-1 - Receipt and initial review.

Code of Federal Regulations, 2013 CFR

2013-10-01

... CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Unsolicited Proposals 15.606-1 Receipt and... information for evaluation; (5) Has overall scientific, technical, or socioeconomic merit; (6) Has been...

48 CFR 15.606-1 - Receipt and initial review.

Code of Federal Regulations, 2014 CFR

2014-10-01

... CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Unsolicited Proposals 15.606-1 Receipt and... information for evaluation; (5) Has overall scientific, technical, or socioeconomic merit; (6) Has been...

Apollo: a sequence annotation editor

PubMed Central

Lewis, SE; Searle, SMJ; Harris, N; Gibson, M; Iyer, V; Richter, J; Wiel, C; Bayraktaroglu, L; Birney, E; Crosby, MA; Kaminker, JS; Matthews, BB; Prochnik, SE; Smith, CD; Tupy, JL; Rubin, GM; Misra, S; Mungall, CJ; Clamp, ME

2002-01-01

The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects. PMID:12537571

Modeling multiple time series annotations as noisy distortions of the ground truth: An Expectation-Maximization approach.

PubMed

Gupta, Rahul; Audhkhasi, Kartik; Jacokes, Zach; Rozga, Agata; Narayanan, Shrikanth

2018-01-01

Studies of time-continuous human behavioral phenomena often rely on ratings from multiple annotators. Since the ground truth of the target construct is often latent, the standard practice is to use ad-hoc metrics (such as averaging annotator ratings). Despite being easy to compute, such metrics may not provide accurate representations of the underlying construct. In this paper, we present a novel method for modeling multiple time series annotations over a continuous variable that computes the ground truth by modeling annotator specific distortions. We condition the ground truth on a set of features extracted from the data and further assume that the annotators provide their ratings as modification of the ground truth, with each annotator having specific distortion tendencies. We train the model using an Expectation-Maximization based algorithm and evaluate it on a study involving natural interaction between a child and a psychologist, to predict confidence ratings of the children's smiles. We compare and analyze the model against two baselines where: (i) the ground truth in considered to be framewise mean of ratings from various annotators and, (ii) each annotator is assumed to bear a distinct time delay in annotation and their annotations are aligned before computing the framewise mean.

Automated Update, Revision, and Quality Control of the Maize Genome Annotations Using MAKER-P Improves the B73 RefGen_v3 Gene Models and Identifies New Genes1[OPEN

PubMed Central

Law, MeiYee; Childs, Kevin L.; Campbell, Michael S.; Stein, Joshua C.; Olson, Andrew J.; Holt, Carson; Panchy, Nicholas; Lei, Jikai; Jiao, Dian; Andorf, Carson M.; Lawrence, Carolyn J.; Ware, Doreen; Shiu, Shin-Han; Sun, Yanni; Jiang, Ning; Yandell, Mark

2015-01-01

The large size and relative complexity of many plant genomes make creation, quality control, and dissemination of high-quality gene structure annotations challenging. In response, we have developed MAKER-P, a fast and easy-to-use genome annotation engine for plants. Here, we report the use of MAKER-P to update and revise the maize (Zea mays) B73 RefGen_v3 annotation build (5b+) in less than 3 h using the iPlant Cyberinfrastructure. MAKER-P identified and annotated 4,466 additional, well-supported protein-coding genes not present in the 5b+ annotation build, added additional untranslated regions to 1,393 5b+ gene models, identified 2,647 5b+ gene models that lack any supporting evidence (despite the use of large and diverse evidence data sets), identified 104,215 pseudogene fragments, and created an additional 2,522 noncoding gene annotations. We also describe a method for de novo training of MAKER-P for the annotation of newly sequenced grass genomes. Collectively, these results lead to the 6a maize genome annotation and demonstrate the utility of MAKER-P for rapid annotation, management, and quality control of grasses and other difficult-to-annotate plant genomes. PMID:25384563

Applying the Karma Provenance tool to NASA's AMSR-E Data Production Stream

NASA Astrophysics Data System (ADS)

Ramachandran, R.; Conover, H.; Regner, K.; Movva, S.; Goodman, H. M.; Pale, B.; Purohit, P.; Sun, Y.

2010-12-01

Current procedures for capturing and disseminating provenance, or data product lineage, are limited in both what is captured and how it is disseminated to the science community. For example, the Advanced Microwave Scanning Radiometer for the Earth Observing System (AMSR-E) Science Investigator-led Processing System (SIPS) generates Level 2 and Level 3 data products for a variety of geophysical parameters. Data provenance and quality information for these data sets is either very general (e.g., user guides, a list of anomalous data receipt and processing conditions over the life of the missions) or difficult to access or interpret (e.g., quality flags embedded in the data, production history files not easily available to users). Karma is a provenance collection and representation tool designed and developed for data driven workflows such as the productions streams used to produce EOS standard products. Karma records uniform and usable provenance metadata independent of the processing system while minimizing both the modification burden on the processing system and the overall performance overhead. Karma collects both the process and data provenance. The process provenance contains information about the workflow execution and the associated algorithm invocations. The data provenance captures metadata about the derivation history of the data product, including algorithms used and input data sources transformed to generate it. As part of an ongoing NASA funded project, Karma is being integrated into the AMSR-E SIPS data production streams. Metadata gathered by the tool will be presented to the data consumers as provenance graphs, which are useful in validating the workflows and determining the quality of the data product. This presentation will discuss design and implementation issues faced while incorporating a provenance tool into a structured data production flow. Prototype results will also be presented in this talk.

Cross-organism learning method to discover new gene functionalities.

PubMed

Domeniconi, Giacomo; Masseroli, Marco; Moro, Gianluca; Pinoli, Pietro

2016-04-01

Knowledge of gene and protein functions is paramount for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. Analyses for biomedical knowledge discovery greatly benefit from the availability of gene and protein functional feature descriptions expressed through controlled terminologies and ontologies, i.e., of gene and protein biomedical controlled annotations. In the last years, several databases of such annotations have become available; yet, these valuable annotations are incomplete, include errors and only some of them represent highly reliable human curated information. Computational techniques able to reliably predict new gene or protein annotations with an associated likelihood value are thus paramount. Here, we propose a novel cross-organisms learning approach to reliably predict new functionalities for the genes of an organism based on the known controlled annotations of the genes of another, evolutionarily related and better studied, organism. We leverage a new representation of the annotation discovery problem and a random perturbation of the available controlled annotations to allow the application of supervised algorithms to predict with good accuracy unknown gene annotations. Taking advantage of the numerous gene annotations available for a well-studied organism, our cross-organisms learning method creates and trains better prediction models, which can then be applied to predict new gene annotations of a target organism. We tested and compared our method with the equivalent single organism approach on different gene annotation datasets of five evolutionarily related organisms (Homo sapiens, Mus musculus, Bos taurus, Gallus gallus and Dictyostelium discoideum). Results show both the usefulness of the perturbation method of available annotations for better prediction model training and a great improvement of the cross-organism models with respect to the single-organism ones, without influence of the evolutionary distance between the considered organisms. The generated ranked lists of reliably predicted annotations, which describe novel gene functionalities and have an associated likelihood value, are very valuable both to complement available annotations, for better coverage in biomedical knowledge discovery analyses, and to quicken the annotation curation process, by focusing it on the prioritized novel annotations predicted. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

48 CFR 315.606-1 - Receipt and initial review.

Code of Federal Regulations, 2012 CFR

2012-10-01

... CONTRACTING METHODS AND CONTRACT TYPES CONTRACTING BY NEGOTIATION Unsolicited Proposals 315.606-1 Receipt and... unsolicited proposals that have been rejected for grant awards due to lack of scientific merit. ...