Aggregating Data for Computational Toxicology Applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System

PubMed Central

Judson, Richard S.; Martin, Matthew T.; Egeghy, Peter; Gangwal, Sumit; Reif, David M.; Kothiya, Parth; Wolf, Maritja; Cathey, Tommy; Transue, Thomas; Smith, Doris; Vail, James; Frame, Alicia; Mosher, Shad; Cohen Hubal, Elaine A.; Richard, Ann M.

2012-01-01

Computational toxicology combines data from high-throughput test methods, chemical structure analyses and other biological domains (e.g., genes, proteins, cells, tissues) with the goals of predicting and understanding the underlying mechanistic causes of chemical toxicity and for predicting toxicity of new chemicals and products. A key feature of such approaches is their reliance on knowledge extracted from large collections of data and data sets in computable formats. The U.S. Environmental Protection Agency (EPA) has developed a large data resource called ACToR (Aggregated Computational Toxicology Resource) to support these data-intensive efforts. ACToR comprises four main repositories: core ACToR (chemical identifiers and structures, and summary data on hazard, exposure, use, and other domains), ToxRefDB (Toxicity Reference Database, a compilation of detailed in vivo toxicity data from guideline studies), ExpoCastDB (detailed human exposure data from observational studies of selected chemicals), and ToxCastDB (data from high-throughput screening programs, including links to underlying biological information related to genes and pathways). The EPA DSSTox (Distributed Structure-Searchable Toxicity) program provides expert-reviewed chemical structures and associated information for these and other high-interest public inventories. Overall, the ACToR system contains information on about 400,000 chemicals from 1100 different sources. The entire system is built using open source tools and is freely available to download. This review describes the organization of the data repository and provides selected examples of use cases. PMID:22408426

Aggregating data for computational toxicology applications: The U.S. Environmental Protection Agency (EPA) Aggregated Computational Toxicology Resource (ACToR) System.

PubMed

Judson, Richard S; Martin, Matthew T; Egeghy, Peter; Gangwal, Sumit; Reif, David M; Kothiya, Parth; Wolf, Maritja; Cathey, Tommy; Transue, Thomas; Smith, Doris; Vail, James; Frame, Alicia; Mosher, Shad; Cohen Hubal, Elaine A; Richard, Ann M

2012-01-01

Computational toxicology combines data from high-throughput test methods, chemical structure analyses and other biological domains (e.g., genes, proteins, cells, tissues) with the goals of predicting and understanding the underlying mechanistic causes of chemical toxicity and for predicting toxicity of new chemicals and products. A key feature of such approaches is their reliance on knowledge extracted from large collections of data and data sets in computable formats. The U.S. Environmental Protection Agency (EPA) has developed a large data resource called ACToR (Aggregated Computational Toxicology Resource) to support these data-intensive efforts. ACToR comprises four main repositories: core ACToR (chemical identifiers and structures, and summary data on hazard, exposure, use, and other domains), ToxRefDB (Toxicity Reference Database, a compilation of detailed in vivo toxicity data from guideline studies), ExpoCastDB (detailed human exposure data from observational studies of selected chemicals), and ToxCastDB (data from high-throughput screening programs, including links to underlying biological information related to genes and pathways). The EPA DSSTox (Distributed Structure-Searchable Toxicity) program provides expert-reviewed chemical structures and associated information for these and other high-interest public inventories. Overall, the ACToR system contains information on about 400,000 chemicals from 1100 different sources. The entire system is built using open source tools and is freely available to download. This review describes the organization of the data repository and provides selected examples of use cases.

A novel approach: chemical relational databases, and the role of the ISSCAN database on assessing chemical carcinogenicity.

PubMed

Benigni, Romualdo; Bossa, Cecilia; Richard, Ann M; Yang, Chihae

2008-01-01

Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did not contain chemical structures. Concepts and technologies originated from the structure-activity relationships science have provided powerful tools to create new types of databases, where the effective linkage of chemical toxicity with chemical structure can facilitate and greatly enhance data gathering and hypothesis generation, by permitting: a) exploration across both chemical and biological domains; and b) structure-searchability through the data. This paper reviews the main public databases, together with the progress in the field of chemical relational databases, and presents the ISSCAN database on experimental chemical carcinogens.

Environmental Chemistry Compound Identification Using High ...

EPA Pesticide Factsheets

There is a growing need for rapid chemical screening and prioritization to inform regulatory decision-making on thousands of chemicals in the environment. We have previously used high-resolution mass spectrometry to examine household vacuum dust samples using liquid chromatography time-of-flight mass spectrometry (LC-TOF/MS). Using a combination of exact mass, isotope distribution, and isotope spacing, molecular features were matched with a list of chemical formulas from the EPA’s Distributed Structure-Searchable Toxicity (DSSTox) database. This has further developed our understanding of how openly available chemical databases, together with the appropriate searches, could be used for the purpose of compound identification. We report here on the utility of the EPA’s iCSS Chemistry Dashboard for the purpose of compound identification using searches against a database of over 720,000 chemicals. We also examine the benefits of QSAR prediction for the purpose of retention time prediction to allow for alignment of both chromatographic and mass spectral properties. This abstract does not reflect U.S. EPA policy presentation at the Eastern Analytical Symposium.

A Layered Searchable Encryption Scheme with Functional Components Independent of Encryption Methods

PubMed Central

Luo, Guangchun; Qin, Ke

2014-01-01

Searchable encryption technique enables the users to securely store and search their documents over the remote semitrusted server, which is especially suitable for protecting sensitive data in the cloud. However, various settings (based on symmetric or asymmetric encryption) and functionalities (ranked keyword query, range query, phrase query, etc.) are often realized by different methods with different searchable structures that are generally not compatible with each other, which limits the scope of application and hinders the functional extensions. We prove that asymmetric searchable structure could be converted to symmetric structure, and functions could be modeled separately apart from the core searchable structure. Based on this observation, we propose a layered searchable encryption (LSE) scheme, which provides compatibility, flexibility, and security for various settings and functionalities. In this scheme, the outputs of the core searchable component based on either symmetric or asymmetric setting are converted to some uniform mappings, which are then transmitted to loosely coupled functional components to further filter the results. In such a way, all functional components could directly support both symmetric and asymmetric settings. Based on LSE, we propose two representative and novel constructions for ranked keyword query (previously only available in symmetric scheme) and range query (previously only available in asymmetric scheme). PMID:24719565

Toxico-Cheminformatics: New and Expanding Public ...

EPA Pesticide Factsheets

High-throughput screening (HTS) technologies, along with efforts to improve public access to chemical toxicity information resources and to systematize older toxicity studies, have the potential to significantly improve information gathering efforts for chemical assessments and predictive capabilities in toxicology. Important developments include: 1) large and growing public resources that link chemical structures to biological activity and toxicity data in searchable format, and that offer more nuanced and varied representations of activity; 2) standardized relational data models that capture relevant details of chemical treatment and effects of published in vivo experiments; and 3) the generation of large amounts of new data from public efforts that are employing HTS technologies to probe a wide range of bioactivity and cellular processes across large swaths of chemical space. By annotating toxicity data with associated chemical structure information, these efforts link data across diverse study domains (e.g., ‘omics’, HTS, traditional toxicity studies), toxicity domains (carcinogenicity, developmental toxicity, neurotoxicity, immunotoxicity, etc) and database sources (EPA, FDA, NCI, DSSTox, PubChem, GEO, ArrayExpress, etc.). Public initiatives are developing systematized data models of toxicity study areas and introducing standardized templates, controlled vocabularies, hierarchical organization, and powerful relational searching capability across capt

Aggregated Computational Toxicology Online Resource

EPA Pesticide Factsheets

Aggregated Computational Toxicology Online Resource (AcTOR) is EPA's online aggregator of all the public sources of chemical toxicity data. ACToR aggregates data from over 1,000 public sources on over 500,000 chemicals and is searchable by chemical name, other identifiers and by chemical structure. It can be used to query a specific chemical and find all publicly available hazard, exposure and risk assessment data. It also provides access to EPA's ToxCast, ToxRefDB, DSSTox, Dashboard and DSSTox data.

New Toxico-Cheminformatics & Computational Toxicology ...

EPA Pesticide Factsheets

EPA’s National Center for Computational Toxicology is building capabilities to support a new paradigm for toxicity screening and prediction. The DSSTox project is improving public access to quality structure-annotated chemical toxicity information in less summarized forms than traditionally employed in SAR modeling, and in ways that facilitate data-mining, and data read-across. The DSSTox Structure-Browser provides structure searchability across all published DSSTox toxicity-related inventory, and is enabling linkages between previously isolated toxicity data resources. As of early March 2008, the public DSSTox inventory has been integrated into PubChem, allowing a user to take full advantage of PubChem structure-activity and bioassay clustering features. The most recent DSSTox version of the Carcinogenic Potency Database file (CPDBAS) illustrates ways in which various summary definitions of carcinogenic activity can be employed in modeling and data mining. Phase I of the ToxCastTM project is generating high-throughput screening data from several hundred biochemical and cell-based assays for a set of 320 chemicals, mostly pesticide actives, with rich toxicology profiles. Incorporating and expanding traditional SAR concepts into this new high-throughput and data-rich world pose conceptual and practical challenges, but also holds great promise for improving predictive capabilities.

Recent Developments in Toxico-Cheminformatics; Supporting ...

EPA Pesticide Factsheets

EPA's National Center for Computational Toxicology is building capabilities to support a new paradigm for toxicity screening and prediction through the harnessing of legacy toxicity data, creation of data linkages, and generation of new high-content and high-thoughput screening data. In association with EPA's ToxCast, ToxRefDB, and ACToR projects, the DSSTox project provides cheminformatics support and, in addition, is improving public access to quality structure-annotated chemical toxicity information in less summarized forms than traditionally employed in SAR modeling, and in ways that facilitate data-mining and data read-across. The latest DSSTox version of the Carcinogenic Potency Database file (CPDBAS) illustrates ways in which various summary definitions of carcinogenic activity can be employed in modeling and data mining. DSSTox Structure-Browser provides structure searchability across all published DSSTox toxicity-related inventory, and is enabling linkages between previously isolated toxicity data resources associated with environmental and industrial chemicals. The public DSSTox inventory also has been integrated into PubChem, allowing a user to take full advantage of PubChem structure-activity and bioassay clustering features. Phase I of the ToxCast project is generating high-throughput screening data from several hundred biochemical and cell-based assays for a set of 320 chemicals, mostly pesticide actives with rich toxicology profiles. Incorporating

Application of Functional Use Predictions to Aid in Structure ...

EPA Pesticide Factsheets

Humans are potentially exposed to thousands of anthropogenic chemicals in commerce. Recent work has shown that the bulk of this exposure may occur in near-field indoor environments (e.g., home, school, work, etc.). Advances in suspect screening analyses (SSA) now allow an improved understanding of the chemicals present in these environments. However, due to the nature of suspect screening techniques, investigators are often left with chemical formula predictions, with the possibility of many chemical structures matching to each formula. Here, newly developed quantitative structure-use relationship (QSUR) models are used to identify potential exposure sources for candidate structures. Previously, a suspect screening workflow was introduced and applied to house dust samples collected from the U.S. Department of Housing and Urban Development’s American Healthy Homes Survey (AHHS) [Rager, et al., Env. Int. 88 (2016)]. This workflow utilized the US EPA’s Distributed Structure-Searchable Toxicity (DSSTox) Database to link identified molecular features to molecular formulas, and ultimately chemical structures. Multiple QSUR models were applied to support the evaluation of candidate structures. These QSURs predict the likelihood of a chemical having a functional use commonly associated with consumer products having near-field use. For 3,228 structures identified as possible chemicals in AHHS house dust samples, we were able to obtain the required descriptors to appl

Linking high resolution mass spectrometry data with exposure and toxicity forecasts to advance high-throughput environmental monitoring

EPA Pesticide Factsheets

There is a growing need in the field of exposure science for monitoring methods that rapidly screen environmental media for suspect contaminants. Measurement and analysis platforms, based on high resolution mass spectrometry (HRMS), now exist to meet this need. Here we describe results of a study that links HRMS data with exposure predictions from the U.S. EPA's ExpoCast? program and in vitro bioassay data from the U.S. interagency Tox21 consortium. Vacuum dust samples were collected from 56 households across the U.S. as part of the American Healthy Homes Survey (AHHS). Sample extracts were analyzed using liquid chromatography time-of-flight mass spectrometry (LC??TOF/MS) with electrospray ionization. On average, approximately 2000 molecular features were identified per sample (based on accurate mass) in negative ion mode, and 3000 in positive ion mode. Exact mass, isotope distribution, and isotope spacing were used to match molecular features with a unique listing of chemical formulas extracted from EPA's Distributed Structure-Searchable Toxicity (DSSTox) database. A total of 978 DSSTox formulas were consistent with the dust LC??TOF/molecular feature data (match score ? 90); these formulas mapped to 3228 possible chemicals in the database. Correct assignment of a unique chemical to a given formula required additional validation steps. Each suspect chemical was prioritized for follow-up confirmation using abundance and detection frequency results, along with exp

EPA Project Updates: DSSTox and ToxCast Generating New ...

EPA Pesticide Factsheets

EPAs National Center for Computational Toxicology is building capabilities to support a new paradigm for toxicity screening and prediction. The DSSTox project is improving public access to quality structure-annotated chemical toxicity information in less summarized forms than traditionally employed in SAR modeling, and in ways that facilitate data-mining, and data read-across. The DSSTox Structure-Browser, launched in September 2007, provides structure searchability across all published DSSTox toxicity-related inventory, and is enabling linkages between previously isolated toxicity data resources. As of early March 2008, the public DSSTox inventory as been integrated into PubChem, allowing a user to take full advantage of PubChem structure-activity and bioassay clustering features. The most recent DSSTox version of Carcinogenic Potency Database file (CPDBAS) illustrates ways in which various summary definitions of carcinogenic activity can be employed in modeling and data mining. Phase I of the ToxCast project is generating high-throughput screening data from several hundred biochemical and cell-based assays for a set of 320 chemicals, mostly pesticide actives, with rich toxicology profiles. Incorporating and expanding traditional SAR Concepts into this new high-throughput and data-rich would pose conceptual and practical challenges, but also holds great promise for improving predictive capabilities. EPA's National Center for Computational Toxicology is bu

Recent Developments in Toxico-Cheminformatics: A New ...

EPA Pesticide Factsheets

Efforts to improve public access to chemical toxicity information resources, coupled with new high-throughput screening (HTS) data and efforts to systematize legacy toxicity studies, have the potential to significantly improve predictive capabilities in toxicology. Important recent developments include: 1) large and growing public resources that link chemical structures to biological activity and toxicity data in searchable format, and that offer more nuanced and varied representations of activity; 2) standardized relational data models that capture relevant details of chemical treatment and effects of published in vivo experiments; and 3) the generation of large amounts of new data from public efforts that are employing HTS technologies to probe a wide range of bioactivity and cellular processes across large swaths of chemical space. Most recently, EPA’s DSSTox project has published several new EPA chemical data inventories (IRIS, HPV, ToxCast) and added an on-line capability for structure (substructure or similarity)-searching through all or parts of the published DSSTox data files. These efforts are, for the first time in many cases, opening up a structure-paved two-way highway between previously inaccessible or isolated public chemical data repositories and large public resources, such as PubChem. In addition, public initiatives (such as ToxML) are developing systematized data models of toxicity study areas, and introducing standardized templates, contr

EPA DSSTox and ToxCast Project Updates: Generating New ...

EPA Pesticide Factsheets

EPA’s National Center for Computational Toxicology is generating data and capabilities to support a new paradigm for toxicity screening and prediction. The DSSTox project is improving public access to quality structure-annotated chemical toxicity information in less summarized forms than traditionally employed in SAR modeling, and in ways that facilitate data-mining and data read-across. The DSSTox Structure-Browser provides structure searchability across the full published DSSTox toxicity-related inventory, enables linkages to and from previously isolated toxicity data resources (soon to include public microarray resources GEO, ArrayExpress, and CEBS), and provides link-outs to cross-indexed public resources such as PubChem, ChemSpider, and ACToR. The published DSSTox inventory and bioassay information also have been integrated into PubChem allowing a user to take full advantage of PubChem structure-activity and bioassay clustering features. Phase I of the ToxCastTM project has generated high-throughput screening (HTS) data from several hundred biochemical and cell-based assays for a set of 320 chemicals, mostly pesticide actives, with rich toxicology profiles. DSSTox and ACToR are providing the primary cheminformatics support for ToxCastTM and collaborative efforts with the National Toxicology Program’s HTS Program and the NIH Chemical Genomics Center. DSSTox will also be a primary vehicle for publishing ToxCastTM ToxRef summarized bioassay data for use

A PATO-compliant zebrafish screening database (MODB): management of morpholino knockdown screen information.

PubMed

Knowlton, Michelle N; Li, Tongbin; Ren, Yongliang; Bill, Brent R; Ellis, Lynda Bm; Ekker, Stephen C

2008-01-07

The zebrafish is a powerful model vertebrate amenable to high throughput in vivo genetic analyses. Examples include reverse genetic screens using morpholino knockdown, expression-based screening using enhancer trapping and forward genetic screening using transposon insertional mutagenesis. We have created a database to facilitate web-based distribution of data from such genetic studies. The MOrpholino DataBase is a MySQL relational database with an online, PHP interface. Multiple quality control levels allow differential access to data in raw and finished formats. MODBv1 includes sequence information relating to almost 800 morpholinos and their targets and phenotypic data regarding the dose effect of each morpholino (mortality, toxicity and defects). To improve the searchability of this database, we have incorporated a fixed-vocabulary defect ontology that allows for the organization of morpholino affects based on anatomical structure affected and defect produced. This also allows comparison between species utilizing Phenotypic Attribute Trait Ontology (PATO) designated terminology. MODB is also cross-linked with ZFIN, allowing full searches between the two databases. MODB offers users the ability to retrieve morpholino data by sequence of morpholino or target, name of target, anatomical structure affected and defect produced. MODB data can be used for functional genomic analysis of morpholino design to maximize efficacy and minimize toxicity. MODB also serves as a template for future sequence-based functional genetic screen databases, and it is currently being used as a model for the creation of a mutagenic insertional transposon database.

Development of an In Silico Metabolic Simulator and Searchable Metabolism Database for Chemical Risk Assessments

EPA Science Inventory

The US EPA is faced with long lists of chemicals that need to be assessed for hazard, and a gap in evaluating chemical risk is accounting for metabolic activation resulting in increased toxicity. The goals of this project are to develop a capability to predict metabolic maps of x...

Linking high resolution mass spectrometry data with exposure ...

EPA Pesticide Factsheets

There is a growing need in the field of exposure science for monitoring methods that rapidly screen environmental media for suspect contaminants. Measurement and analysis platforms, based on high resolution mass spectrometry (HRMS), now exist to meet this need. Here we describe results of a study that links HRMS data with exposure predictions from the U.S. EPA's ExpoCast™ program and in vitro bioassay data from the U.S. interagency Tox21 consortium. Vacuum dust samples were collected from 56 households across the U.S. as part of the American Healthy Homes Survey (AHHS). Sample extracts were analyzed using liquid chromatography time-of-flight mass spectrometry (LC–TOF/MS) with electrospray ionization. On average, approximately 2000 molecular features were identified per sample (based on accurate mass) in negative ion mode, and 3000 in positive ion mode. Exact mass, isotope distribution, and isotope spacing were used to match molecular features with a unique listing of chemical formulas extracted from EPA's Distributed Structure-Searchable Toxicity (DSSTox) database. A total of 978 DSSTox formulas were consistent with the dust LC–TOF/molecular feature data (match score ≥ 90); these formulas mapped to 3228 possible chemicals in the database. Correct assignment of a unique chemical to a given formula required additional validation steps. Each suspect chemical was prioritized for follow-up confirmation using abundance and detection frequency results, along wi

ToxRefDB - Release user-friendly web-based tool for mining ToxRefDB

EPA Science Inventory

The updated URL link is for a table of NCCT ToxCast public datasets. The next to last row of the table has the link for the US EPA ToxCast ToxRefDB Data Release October 2014. ToxRefDB provides detailed chemical toxicity data in a publically accessible searchable format. ToxRefD...

Distribution and Features of the Six Classes of Peroxiredoxins

PubMed Central

Poole, Leslie B.; Nelson, Kimberly J.

2016-01-01

Peroxiredoxins are cysteine-dependent peroxide reductases that group into 6 different, structurally discernable classes. In 2011, our research team reported the application of a bioinformatic approach called active site profiling to extract active site-proximal sequence segments from the 29 distinct, structurally-characterized peroxiredoxins available at the time. These extracted sequences were then used to create unique profiles for the six groups which were subsequently used to search GenBank(nr), allowing identification of ∼3500 peroxiredoxin sequences and their respective subgroups. Summarized in this minireview are the features and phylogenetic distributions of each of these peroxiredoxin subgroups; an example is also provided illustrating the use of the web accessible, searchable database known as PREX to identify subfamily-specific peroxiredoxin sequences for the organism Vitis vinifera (grape). PMID:26810075

Rapid experimental measurements of physicochemical properties to inform models and testing.

PubMed

Nicolas, Chantel I; Mansouri, Kamel; Phillips, Katherine A; Grulke, Christopher M; Richard, Ann M; Williams, Antony J; Rabinowitz, James; Isaacs, Kristin K; Yau, Alice; Wambaugh, John F

2018-05-02

The structures and physicochemical properties of chemicals are important for determining their potential toxicological effects, toxicokinetics, and route(s) of exposure. These data are needed to prioritize the risk for thousands of environmental chemicals, but experimental values are often lacking. In an attempt to efficiently fill data gaps in physicochemical property information, we generated new data for 200 structurally diverse compounds, which were rigorously selected from the USEPA ToxCast chemical library, and whose structures are available within the Distributed Structure-Searchable Toxicity Database (DSSTox). This pilot study evaluated rapid experimental methods to determine five physicochemical properties, including the log of the octanol:water partition coefficient (known as log(K ow ) or logP), vapor pressure, water solubility, Henry's law constant, and the acid dissociation constant (pKa). For most compounds, experiments were successful for at least one property; log(K ow ) yielded the largest return (176 values). It was determined that 77 ToxPrint structural features were enriched in chemicals with at least one measurement failure, indicating which features may have played a role in rapid method failures. To gauge consistency with traditional measurement methods, the new measurements were compared with previous measurements (where available). Since quantitative structure-activity/property relationship (QSAR/QSPR) models are used to fill gaps in physicochemical property information, 5 suites of QSPRs were evaluated for their predictive ability and chemical coverage or applicability domain of new experimental measurements. The ability to have accurate measurements of these properties will facilitate better exposure predictions in two ways: 1) direct input of these experimental measurements into exposure models; and 2) construction of QSPRs with a wider applicability domain, as their predicted physicochemical values can be used to parameterize exposure models in the absence of experimental data. Published by Elsevier B.V.

The anatomy of urban social networks and its implications in the searchability problem

PubMed Central

Herrera-Yagüe, C.; Schneider, C. M.; Couronné, T.; Smoreda, Z.; Benito, R. M.; Zufiria, P. J.; González, M. C.

2015-01-01

The appearance of large geolocated communication datasets has recently increased our understanding of how social networks relate to their physical space. However, many recurrently reported properties, such as the spatial clustering of network communities, have not yet been systematically tested at different scales. In this work we analyze the social network structure of over 25 million phone users from three countries at three different scales: country, provinces and cities. We consistently find that this last urban scenario presents significant differences to common knowledge about social networks. First, the emergence of a giant component in the network seems to be controlled by whether or not the network spans over the entire urban border, almost independently of the population or geographic extension of the city. Second, urban communities are much less geographically clustered than expected. These two findings shed new light on the widely-studied searchability in self-organized networks. By exhaustive simulation of decentralized search strategies we conclude that urban networks are searchable not through geographical proximity as their country-wide counterparts, but through an homophily-driven community structure. PMID:26035529

The anatomy of urban social networks and its implications in the searchability problem.

PubMed

Herrera-Yagüe, C; Schneider, C M; Couronné, T; Smoreda, Z; Benito, R M; Zufiria, P J; González, M C

2015-06-02

The appearance of large geolocated communication datasets has recently increased our understanding of how social networks relate to their physical space. However, many recurrently reported properties, such as the spatial clustering of network communities, have not yet been systematically tested at different scales. In this work we analyze the social network structure of over 25 million phone users from three countries at three different scales: country, provinces and cities. We consistently find that this last urban scenario presents significant differences to common knowledge about social networks. First, the emergence of a giant component in the network seems to be controlled by whether or not the network spans over the entire urban border, almost independently of the population or geographic extension of the city. Second, urban communities are much less geographically clustered than expected. These two findings shed new light on the widely-studied searchability in self-organized networks. By exhaustive simulation of decentralized search strategies we conclude that urban networks are searchable not through geographical proximity as their country-wide counterparts, but through an homophily-driven community structure.

Investigation and risk evaluation of the occurrence of carbamazepine, oxcarbazepine, their human metabolites and transformation products in the urban water cycle.

PubMed

Brezina, Elena; Prasse, Carsten; Meyer, Johannes; Mückter, Harald; Ternes, Thomas A

2017-06-01

Trace organic contaminants such as pharmaceuticals, personal care products and industrial chemicals are frequently detected in the urban water cycle, including wastewater, surface water and groundwater, as well as drinking water. These also include human metabolites (HMs), which are formed in the human body and then excreted via urine or feces, as well as transformation products (TPs) formed in engineered treatment systems and the aquatic environment. In the current study, the occurrence of HMs as well as their TPs of the anticonvulsants carbamazepine (CBZ) and oxcarbazepine (OXC) were investigated using LC tandem MS in effluents of wastewater treatment plants (WWTPs), surface water and groundwater. Highest concentrations were observed in raw wastewater for 10,11-dihydro-10,11-dihydroxycarbamazepine (DiOHCBZ), 10,11-dihydro-10-hydroxy-cabamazepine (10OHCBZ) and CBZ with concentrations ranging up to 2.7 ± 0.4, 1.7 ± 0.2 and 1.07 ± 0.06 μg L -1 , respectively. Predictions of different toxicity endpoints using a Distributed Structure-Searchable Toxicity (DSSTox) expert system query indicated that several HMs and TPs, in particular 9-carboxy-acridine (9-CA-ADIN) and acridone (ADON), may exhibit an increased genotoxicity compared to the parent compound CBZ. As 9-CA-ADIN was also detected in groundwater, a detailed investigation of the genotoxicity of 9-CA-ADIN is warranted. Investigations of an advanced wastewater treatment plant further revealed that the discharge of the investigated compounds into the aquatic environment could be substantially reduced by ozonation followed by granular activated carbon (GAC) filtration. Copyright © 2016 Elsevier Ltd. All rights reserved.

Computational toxicology as implemented by the U.S. EPA: providing high throughput decision support tools for screening and assessing chemical exposure, hazard and risk.

PubMed

Kavlock, Robert; Dix, David

2010-02-01

Computational toxicology is the application of mathematical and computer models to help assess chemical hazards and risks to human health and the environment. Supported by advances in informatics, high-throughput screening (HTS) technologies, and systems biology, the U.S. Environmental Protection Agency EPA is developing robust and flexible computational tools that can be applied to the thousands of chemicals in commerce, and contaminant mixtures found in air, water, and hazardous-waste sites. The Office of Research and Development (ORD) Computational Toxicology Research Program (CTRP) is composed of three main elements. The largest component is the National Center for Computational Toxicology (NCCT), which was established in 2005 to coordinate research on chemical screening and prioritization, informatics, and systems modeling. The second element consists of related activities in the National Health and Environmental Effects Research Laboratory (NHEERL) and the National Exposure Research Laboratory (NERL). The third and final component consists of academic centers working on various aspects of computational toxicology and funded by the U.S. EPA Science to Achieve Results (STAR) program. Together these elements form the key components in the implementation of both the initial strategy, A Framework for a Computational Toxicology Research Program (U.S. EPA, 2003), and the newly released The U.S. Environmental Protection Agency's Strategic Plan for Evaluating the Toxicity of Chemicals (U.S. EPA, 2009a). Key intramural projects of the CTRP include digitizing legacy toxicity testing information toxicity reference database (ToxRefDB), predicting toxicity (ToxCast) and exposure (ExpoCast), and creating virtual liver (v-Liver) and virtual embryo (v-Embryo) systems models. U.S. EPA-funded STAR centers are also providing bioinformatics, computational toxicology data and models, and developmental toxicity data and models. The models and underlying data are being made publicly available through the Aggregated Computational Toxicology Resource (ACToR), the Distributed Structure-Searchable Toxicity (DSSTox) Database Network, and other U.S. EPA websites. While initially focused on improving the hazard identification process, the CTRP is placing increasing emphasis on using high-throughput bioactivity profiling data in systems modeling to support quantitative risk assessments, and in developing complementary higher throughput exposure models. This integrated approach will enable analysis of life-stage susceptibility, and understanding of the exposures, pathways, and key events by which chemicals exert their toxicity in developing systems (e.g., endocrine-related pathways). The CTRP will be a critical component in next-generation risk assessments utilizing quantitative high-throughput data and providing a much higher capacity for assessing chemical toxicity than is currently available.

Astronomical Software Directory Service

NASA Technical Reports Server (NTRS)

Hanisch, R. J.; Payne, H.; Hayes, J.

1998-01-01

This is the final report on the development of the Astronomical Software Directory Service (ASDS), a distributable, searchable, WWW-based database of software packages and their related documentation. ASDS provides integrated access to 56 astronomical software packages, with more than 16,000 URL's indexed for full-text searching.

ToxicDocs (www.ToxicDocs.org): from history buried in stacks of paper to open, searchable archives online.

PubMed

Rosner, David; Markowitz, Gerald; Chowkwanyun, Merlin

2018-02-01

As a result of a legal mechanism called discovery, the authors accumulated millions of internal corporate and trade association documents related to the introduction of new products and chemicals into workplaces and commerce. What did these private entities discuss among themselves and with their experts? The plethora of documents, both a blessing and a curse, opened new sources and interesting questions about corporate and regulatory histories. But they also posed an almost insurmountable challenge to historians. Thus emerged ToxicDocs, possible only with a technological innovation known as "Big Data." That refers to the sheer volume of new digital data and to the computational power to analyze them. Users will be able to identify what firms knew (or did not know) about the dangers of toxic substances in their products-and when. The database opens many areas to inquiry including environmental studies, business history, government regulation, and public policy. ToxicDocs will remain a resource free and open to all, anywhere in the world.

DEVELOPMENT OF A STRUCTURE-SEARCHABLE DATABASE FOR PESTICIDE METABOLITES AND ENVIRONMENTAL DEGRADATES

EPA Science Inventory

USEPA is modifying and enhancing existing software for the depiction of metabolic maps to provide access via structures to metabolism information and associated data in EPA's Office of Pesticide Programs (OPP). The database includes information submitted to EPA in support of pest...

PSI:Biology-Materials Repository: A Biologist’s Resource for Protein Expression Plasmids

PubMed Central

Cormier, Catherine Y.; Park, Jin G.; Fiacco, Michael; Steel, Jason; Hunter, Preston; Kramer, Jason; Singla, Rajeev; LaBaer, Joshua

2011-01-01

The Protein Structure Initiative:Biology-Materials Repository (PSI:Biology-MR; MR; http://psimr.asu.edu) sequence-verifies, annotates, stores, and distributes the protein expression plasmids and vectors created by the Protein Structure Initiative (PSI). The MR has developed an informatics and sample processing pipeline that manages this process for thousands of samples per month from nearly a dozen PSI centers. DNASU (http://dnasu.asu.edu), a freely searchable database, stores the plasmid annotations, which include the full-length sequence, vector information, and associated publications for over 130,000 plasmids created by our laboratory, by the PSI and other consortia, and by individual laboratories for distribution to researchers worldwide. Each plasmid links to external resources, including the PSI Structural Biology Knowledgebase (http://sbkb.org), which facilitates cross-referencing of a particular plasmid to additional protein annotations and experimental data. To expedite and simplify plasmid requests, the MR uses an expedited material transfer agreement (EP-MTA) network, where researchers from network institutions can order and receive PSI plasmids without institutional delays. Currently over 39,000 protein expression plasmids and 78 empty vectors from the PSI are available upon request from DNASU. Overall, the MR’s repository of expression-ready plasmids, its automated pipeline, and the rapid process for receiving and distributing these plasmids more effectively allows the research community to dissect the biological function of proteins whose structures have been studied by the PSI. PMID:21360289

Protein Structure Initiative Material Repository: an open shared public resource of structural genomics plasmids for the biological community

PubMed Central

Cormier, Catherine Y.; Mohr, Stephanie E.; Zuo, Dongmei; Hu, Yanhui; Rolfs, Andreas; Kramer, Jason; Taycher, Elena; Kelley, Fontina; Fiacco, Michael; Turnbull, Greggory; LaBaer, Joshua

2010-01-01

The Protein Structure Initiative Material Repository (PSI-MR; http://psimr.asu.edu) provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. These plasmids are a resource that allows the research community to dissect the biological function of proteins whose structures have been identified by the PSI. The plasmid annotation, which includes the full length sequence, vector information and associated publications, is stored in a freely available, searchable database called DNASU (http://dnasu.asu.edu). Each PSI plasmid is also linked to a variety of additional resources, which facilitates cross-referencing of a particular plasmid to protein annotations and experimental data. Plasmid samples can be requested directly through the website. We have also developed a novel strategy to avoid the most common concern encountered when distributing plasmids namely, the complexity of material transfer agreement (MTA) processing and the resulting delays this causes. The Expedited Process MTA, in which we created a network of institutions that agree to the terms of transfer in advance of a material request, eliminates these delays. Our hope is that by creating a repository of expression-ready plasmids and expediting the process for receiving these plasmids, we will help accelerate the accessibility and pace of scientific discovery. PMID:19906724

Development of a Searchable Metabolite Database and Simulator of Xenobiotic Metabolism

EPA Science Inventory

A computational tool (MetaPath) has been developed for storage and analysis of metabolic pathways and associated metadata. The system is capable of sophisticated text and chemical structure/substructure searching as well as rapid comparison of metabolites formed across chemicals,...

Transformation of Developmental Neurotoxicity Data into a Structure-Searchable Relational Database

EPA Science Inventory

A database of neurotoxicants is critical to support the development and validation of animal alternatives for neurotoxicity. Validation of in vitro test methods can only be done using known animal and human neurotoxicants producing defined responses for neurochemical, neuropatho...

IDAAPM: integrated database of ADMET and adverse effects of predictive modeling based on FDA approved drug data.

PubMed

Legehar, Ashenafi; Xhaard, Henri; Ghemtio, Leo

2016-01-01

The disposition of a pharmaceutical compound within an organism, i.e. its Absorption, Distribution, Metabolism, Excretion, Toxicity (ADMET) properties and adverse effects, critically affects late stage failure of drug candidates and has led to the withdrawal of approved drugs. Computational methods are effective approaches to reduce the number of safety issues by analyzing possible links between chemical structures and ADMET or adverse effects, but this is limited by the size, quality, and heterogeneity of the data available from individual sources. Thus, large, clean and integrated databases of approved drug data, associated with fast and efficient predictive tools are desirable early in the drug discovery process. We have built a relational database (IDAAPM) to integrate available approved drug data such as drug approval information, ADMET and adverse effects, chemical structures and molecular descriptors, targets, bioactivity and related references. The database has been coupled with a searchable web interface and modern data analytics platform (KNIME) to allow data access, data transformation, initial analysis and further predictive modeling. Data were extracted from FDA resources and supplemented from other publicly available databases. Currently, the database contains information regarding about 19,226 FDA approval applications for 31,815 products (small molecules and biologics) with their approval history, 2505 active ingredients, together with as many ADMET properties, 1629 molecular structures, 2.5 million adverse effects and 36,963 experimental drug-target bioactivity data. IDAAPM is a unique resource that, in a single relational database, provides detailed information on FDA approved drugs including their ADMET properties and adverse effects, the corresponding targets with bioactivity data, coupled with a data analytics platform. It can be used to perform basic to complex drug-target ADMET or adverse effects analysis and predictive modeling. IDAAPM is freely accessible at http://idaapm.helsinki.fi and can be exploited through a KNIME workflow connected to the database.Graphical abstractFDA approved drug data integration for predictive modeling.

Distributed Information Search and Retrieval for Astronomical Resource Discovery and Data Mining

NASA Astrophysics Data System (ADS)

Murtagh, Fionn; Guillaume, Damien

Information search and retrieval has become by nature a distributed task. We look at tools and techniques which are of importance in this area. Current technological evolution can be summarized as the growing stability and cohesiveness of distributed architectures of searchable objects. The objects themselves are more often than not multimedia, including published articles or grey literature reports, yellow page services, image data, catalogs, presentation and online display materials, and ``operations'' information such as scheduling and publicly accessible proposal information. The evolution towards distributed architectures, protocols and formats, and the direction of our own work, are focussed on in this paper.

Forensic Science and the Internet - Current Utilization and Future Potential.

PubMed

Chamakura, R P

1997-12-01

The Internet has become a very powerful and inexpensive tool for the free distribution of knowledge and information. It is a learning and research tool, a virtual library without borders and membership requirements, a help desk, and a publication house providing newspapers with current information and journals with instant publication. Very soon, when live audio and video transmission is perfected, the Internet (popularly referred to as the Net) also will be a live classroom and everyday conference site. This article provides a brief overview of the basic structure and essential components of the Internet. A limited number of home pages/Web sites that are already made available on the Net by scientists, laboratories, and colleges in the forensic science community are presented in table forms. Home pages/Web sites containing useful information pertinent to different disciplines of forensic science are also categorized in various tables. The ease and benefits of the Internet use are exemplified by the author's personal experience. Currently, only a few forensic scientists and institutions have made their presence felt. More participation and active contribution and the creation of on-line searchable databases in all specialties of forensic science are urgently needed. Leading forensic journals should take the lead and create on-line searchable indexes with abstracts. Creating Internet repositories of unpublished papers is an idea worth looking into. Leading forensic science institutions should also develop use of the Net to provide training and retraining opportunities for forensic scientists. Copyright © 1997 Central Police University.

Building up a QSAR model for toxicity toward Tetrahymena pyriformis by the Monte Carlo method: A case of benzene derivatives.

PubMed

Toropova, Alla P; Schultz, Terry W; Toropov, Andrey A

2016-03-01

Data on toxicity toward Tetrahymena pyriformis is indicator of applicability of a substance in ecologic and pharmaceutical aspects. Quantitative structure-activity relationships (QSARs) between the molecular structure of benzene derivatives and toxicity toward T. pyriformis (expressed as the negative logarithms of the population growth inhibition dose, mmol/L) are established. The available data were randomly distributed three times into the visible training and calibration sets, and invisible validation sets. The statistical characteristics for the validation set are the following: r(2)=0.8179 and s=0.338 (first distribution); r(2)=0.8682 and s=0.341 (second distribution); r(2)=0.8435 and s=0.323 (third distribution). These models are built up using only information on the molecular structure: no data on physicochemical parameters, 3D features of the molecular structure and quantum mechanics descriptors are involved in the modeling process. Copyright © 2016 Elsevier B.V. All rights reserved.

Efficiently Multi-User Searchable Encryption Scheme with Attribute Revocation and Grant for Cloud Storage

PubMed Central

Wang, Shangping; Zhang, Xiaoxue; Zhang, Yaling

2016-01-01

Cipher-policy attribute-based encryption (CP-ABE) focus on the problem of access control, and keyword-based searchable encryption scheme focus on the problem of finding the files that the user interested in the cloud storage quickly. To design a searchable and attribute-based encryption scheme is a new challenge. In this paper, we propose an efficiently multi-user searchable attribute-based encryption scheme with attribute revocation and grant for cloud storage. In the new scheme the attribute revocation and grant processes of users are delegated to proxy server. Our scheme supports multi attribute are revoked and granted simultaneously. Moreover, the keyword searchable function is achieved in our proposed scheme. The security of our proposed scheme is reduced to the bilinear Diffie-Hellman (BDH) assumption. Furthermore, the scheme is proven to be secure under the security model of indistinguishability against selective ciphertext-policy and chosen plaintext attack (IND-sCP-CPA). And our scheme is also of semantic security under indistinguishability against chosen keyword attack (IND-CKA) in the random oracle model. PMID:27898703

Efficiently Multi-User Searchable Encryption Scheme with Attribute Revocation and Grant for Cloud Storage.

PubMed

Wang, Shangping; Zhang, Xiaoxue; Zhang, Yaling

2016-01-01

Cipher-policy attribute-based encryption (CP-ABE) focus on the problem of access control, and keyword-based searchable encryption scheme focus on the problem of finding the files that the user interested in the cloud storage quickly. To design a searchable and attribute-based encryption scheme is a new challenge. In this paper, we propose an efficiently multi-user searchable attribute-based encryption scheme with attribute revocation and grant for cloud storage. In the new scheme the attribute revocation and grant processes of users are delegated to proxy server. Our scheme supports multi attribute are revoked and granted simultaneously. Moreover, the keyword searchable function is achieved in our proposed scheme. The security of our proposed scheme is reduced to the bilinear Diffie-Hellman (BDH) assumption. Furthermore, the scheme is proven to be secure under the security model of indistinguishability against selective ciphertext-policy and chosen plaintext attack (IND-sCP-CPA). And our scheme is also of semantic security under indistinguishability against chosen keyword attack (IND-CKA) in the random oracle model.

The U.S. Dairy Forage Research Center (USDFRC) condensed tannin NMR database

USDA-ARS?s Scientific Manuscript database

This perspective describes a solution-state NMR database for flavan-3-ol monomers and condensed tannin dimers through tetramers obtained from the literature to 2015, containing data searchable by structure, molecular formula, degrees of polymerization, 1H and 13C chemical shifts of the condensed tan...

78 FR 77475 - National Institute of Neurological Disorders and Stroke

Federal Register 2010, 2011, 2012, 2013, 2014

2013-12-23

... items including the National Pain Strategy, a searchable data base for the Federally-funded pain... Committee business items including the National Pain Strategy, a searchable data base for the Federally...

Best Practices for Searchable Collection Pages

EPA Pesticide Factsheets

Searchable Collection pages are stand-alone documents that do not have any web area navigation. They should not recreate existing content on other sites and should be tagged with quality metadata and taxonomy terms.

A Prototype Publishing Registry for the Virtual Observatory

NASA Astrophysics Data System (ADS)

Williamson, R.; Plante, R.

2004-07-01

In the Virtual Observatory (VO), a registry helps users locate resources, such as data and services, in a distributed environment. A general framework for VO registries is now under development within the International Virtual Observatory Alliance (IVOA) Registry Working Group. We present a prototype of one component of this framework: the publishing registry. The publishing registry allows data providers to expose metadata descriptions of their resources to the VO environment. Searchable registries can harvest the metadata from many publishing registries and make them searchable by users. We have developed a prototype publishing registry that data providers can install at their sites to publish their resources. The descriptions are exposed using the Open Archive Initiative (OAI) Protocol for Metadata Harvesting. Automating the input of metadata into registries is critical when a provider wishes to describe many resources. We illustrate various strategies for such automation, both currently in use and planned for the future. We also describe how future versions of the registry can adapt automatically to evolving metadata schemas for describing resources.

Evaluation of e-liquid toxicity using an open-source high-throughput screening assay

PubMed Central

Keating, James E.; Zorn, Bryan T.; Kochar, Tavleen K.; Wolfgang, Matthew C.; Glish, Gary L.; Tarran, Robert

2018-01-01

The e-liquids used in electronic cigarettes (E-cigs) consist of propylene glycol (PG), vegetable glycerin (VG), nicotine, and chemical additives for flavoring. There are currently over 7,700 e-liquid flavors available, and while some have been tested for toxicity in the laboratory, most have not. Here, we developed a 3-phase, 384-well, plate-based, high-throughput screening (HTS) assay to rapidly triage and validate the toxicity of multiple e-liquids. Our data demonstrated that the PG/VG vehicle adversely affected cell viability and that a large number of e-liquids were more toxic than PG/VG. We also performed gas chromatography–mass spectrometry (GC-MS) analysis on all tested e-liquids. Subsequent nonmetric multidimensional scaling (NMDS) analysis revealed that e-liquids are an extremely heterogeneous group. Furthermore, these data indicated that (i) the more chemicals contained in an e-liquid, the more toxic it was likely to be and (ii) the presence of vanillin was associated with higher toxicity values. Further analysis of common constituents by electron ionization revealed that the concentration of cinnamaldehyde and vanillin, but not triacetin, correlated with toxicity. We have also developed a publicly available searchable website (www.eliquidinfo.org). Given the large numbers of available e-liquids, this website will serve as a resource to facilitate dissemination of this information. Our data suggest that an HTS approach to evaluate the toxicity of multiple e-liquids is feasible. Such an approach may serve as a roadmap to enable bodies such as the Food and Drug Administration (FDA) to better regulate e-liquid composition. PMID:29584716

DSSTOX WEBSITE LAUNCH: IMPROVING PUBLIC ACCESS TO DATABASES FOR BUILDING STRUCTURE-TOXICITY PREDICTION MODELS

EPA Science Inventory

DSSTox Website Launch: Improving Public Access to Databases for Building Structure-Toxicity Prediction Models
Ann M. Richard
US Environmental Protection Agency, Research Triangle Park, NC, USA

Distributed: Decentralized set of standardized, field-delimited databases,...

A Study of Practical Proxy Reencryption with a Keyword Search Scheme considering Cloud Storage Structure

PubMed Central

Lee, Im-Yeong

2014-01-01

Data outsourcing services have emerged with the increasing use of digital information. They can be used to store data from various devices via networks that are easy to access. Unlike existing removable storage systems, storage outsourcing is available to many users because it has no storage limit and does not require a local storage medium. However, the reliability of storage outsourcing has become an important topic because many users employ it to store large volumes of data. To protect against unethical administrators and attackers, a variety of cryptography systems are used, such as searchable encryption and proxy reencryption. However, existing searchable encryption technology is inconvenient for use in storage outsourcing environments where users upload their data to be shared with others as necessary. In addition, some existing schemes are vulnerable to collusion attacks and have computing cost inefficiencies. In this paper, we analyze existing proxy re-encryption with keyword search. PMID:24693240

A study of practical proxy reencryption with a keyword search scheme considering cloud storage structure.

PubMed

Lee, Sun-Ho; Lee, Im-Yeong

2014-01-01

Data outsourcing services have emerged with the increasing use of digital information. They can be used to store data from various devices via networks that are easy to access. Unlike existing removable storage systems, storage outsourcing is available to many users because it has no storage limit and does not require a local storage medium. However, the reliability of storage outsourcing has become an important topic because many users employ it to store large volumes of data. To protect against unethical administrators and attackers, a variety of cryptography systems are used, such as searchable encryption and proxy reencryption. However, existing searchable encryption technology is inconvenient for use in storage outsourcing environments where users upload their data to be shared with others as necessary. In addition, some existing schemes are vulnerable to collusion attacks and have computing cost inefficiencies. In this paper, we analyze existing proxy re-encryption with keyword search.

A Framework for Evaluating Science and Technology Electronic Reference Books: A Comparison of Five Platforms in Chemistry

ERIC Educational Resources Information Center

Lafferty, Meghan

2009-01-01

This article examines what is desirable in online reference books in science and technology and outlines a framework for evaluating their interfaces. The framework considers factors unique to these subject areas like chemical structures and numerical data. Criteria in three categories, navigability, searchability, and results, were applied to five…

EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

NASA Technical Reports Server (NTRS)

Johnston, Stephanie

2016-01-01

The EVA (Extravehicular Activity) Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, searchable repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, the one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision control system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, and also for hundreds of other NASA and contract employees. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

An Efficient Searchable Encryption Against Keyword Guessing Attacks for Sharable Electronic Medical Records in Cloud-based System.

PubMed

Wu, Yilun; Lu, Xicheng; Su, Jinshu; Chen, Peixin

2016-12-01

Preserving the privacy of electronic medical records (EMRs) is extremely important especially when medical systems adopt cloud services to store patients' electronic medical records. Considering both the privacy and the utilization of EMRs, some medical systems apply searchable encryption to encrypt EMRs and enable authorized users to search over these encrypted records. Since individuals would like to share their EMRs with multiple persons, how to design an efficient searchable encryption for sharable EMRs is still a very challenge work. In this paper, we propose a cost-efficient secure channel free searchable encryption (SCF-PEKS) scheme for sharable EMRs. Comparing with existing SCF-PEKS solutions, our scheme reduces the storage overhead and achieves better computation performance. Moreover, our scheme can guard against keyword guessing attack, which is neglected by most of the existing schemes. Finally, we implement both our scheme and a latest medical-based scheme to evaluate the performance. The evaluation results show that our scheme performs much better performance than the latest one for sharable EMRs.

Distributed Common Ground System - Army (DCGS-A) Increment 1 Release 2 Follow-on Operational Test and Evaluation (FOT and E) Report

DTIC Science & Technology

2016-01-01

Moving Target Indicator, Unmanned Aircraft System (UAS), Rivet Joint, U-2, and ground signals intelligence (PROPHET). At the BCT, Ranger Regiment and... metadata catalog managed by the DIB management office (outside of the DCGS-A system ). A metadata is a searchable description of data, and users across...challenge for users . The system required reboots about every 20 hours for users who had heavy workloads such as the fire support analysts and data

Neural network based chemical structure indexing.

PubMed

Rughooputh, S D; Rughooputh, H C

2001-01-01

Searches on chemical databases are presently dominated by the text-based content of a paper which can be indexed into a keyword searchable form. Such traditional searches can prove to be very time-consuming and discouraging to the less frequent scientist. We report a simple chemical indexing based on the molecular structure alone. The method used is based on a one-to-one correspondence between the chemical structure presented as an image to a neural network and the corresponding binary output. The method is direct and less cumbersome (compared with traditional methods) and proves to be robust, elegant, and very versatile.

Improving wilderness stewardship through searchable databases of U.S. legislative history and legislated special provisions

Treesearch

David R. Craig; Peter Landres; Laurie Yung

2010-01-01

The online resource Wilderness.net currently provides quick access to the text of every public law designating wilderness in the U.S. National Wilderness Preservation System (NWPS). This article describes two new searchable databases recently completed and added to the information available on Wilderness.net to help wilderness managers and others understand and...

U.S. Quaternary Fault and Fold Database Released

NASA Astrophysics Data System (ADS)

Haller, Kathleen M.; Machette, Michael N.; Dart, Richard L.; Rhea, B. Susan

2004-06-01

A comprehensive online compilation of Quaternary-age faults and folds throughout the United States was recently released by the U.S. Geological Survey, with cooperation from state geological surveys, academia, and the private sector. The Web site at http://Qfaults.cr.usgs.gov/ contains searchable databases and related geo-spatial data that characterize earthquake-related structures that could be potential seismic sources for large-magnitude (M > 6) earthquakes.

ACToR – Aggregated Computational Toxicology Resource ...

EPA Pesticide Factsheets

ACToR (Aggregated Computational Toxicology Resource) is a collection of databases collated or developed by the US EPA National Center for Computational Toxicology (NCCT). More than 200 sources of publicly available data on environmental chemicals have been brought together and made searchable by chemical name and other identifiers, and by chemical structure. Data includes chemical structure, physico-chemical values, in vitro assay data and in vivo toxicology data. Chemicals include, but are not limited to, high and medium production volume industrial chemicals, pesticides (active and inert ingredients), and potential ground and drinking water contaminants.

The Next Generation of NASA Night Sky Network: A Searchable Nationwide Database of Astronomy Events

NASA Astrophysics Data System (ADS)

Ames, Z.; Berendsen, M.; White, V.

2010-08-01

With support from NASA, the Astronomical Society of the Pacific (ASP) first developed the Night Sky Network (NSN) in 2004. The NSN was created in response to research conducted by the Institute for Learning Innovation (ILI) to determine what type of support amateur astronomers could use to increase the efficiency and extent of their educational outreach programs. Since its creation, the NSN has grown to include an online searchable database of toolkit resources, Presentation Skills Videos covering topics such as working with kids and how to answer difficult questions, and a searchable nationwide calendar of astronomy events that supports club organization. The features of the NSN have allowed the ASP to create a template that amateur science organizations might use to create a similar support network for their members and the public.

Piloting a Searchable Database of Dropout Prevention Programs in Nine Low-Income Urban School Districts in the Northeast and Islands Region. Issues & Answers. REL 2008-No. 046

ERIC Educational Resources Information Center

Myint-U, Athi; O'Donnell, Lydia; Osher, David; Petrosino, Anthony; Stueve, Ann

2008-01-01

Despite evidence that some dropout prevention programs have positive effects, whether districts in the region are using such evidence-based programs has not been documented. To generate and share knowledge on dropout programs and policies, this report details a project to create a searchable database with information on target audiences,…

A keyword searchable attribute-based encryption scheme with attribute update for cloud storage.

PubMed

Wang, Shangping; Ye, Jian; Zhang, Yaling

2018-01-01

Ciphertext-policy attribute-based encryption (CP-ABE) scheme is a new type of data encryption primitive, which is very suitable for data cloud storage for its fine-grained access control. Keyword-based searchable encryption scheme enables users to quickly find interesting data stored in the cloud server without revealing any information of the searched keywords. In this work, we provide a keyword searchable attribute-based encryption scheme with attribute update for cloud storage, which is a combination of attribute-based encryption scheme and keyword searchable encryption scheme. The new scheme supports the user's attribute update, especially in our new scheme when a user's attribute need to be updated, only the user's secret key related with the attribute need to be updated, while other user's secret key and the ciphertexts related with this attribute need not to be updated with the help of the cloud server. In addition, we outsource the operation with high computation cost to cloud server to reduce the user's computational burden. Moreover, our scheme is proven to be semantic security against chosen ciphertext-policy and chosen plaintext attack in the general bilinear group model. And our scheme is also proven to be semantic security against chosen keyword attack under bilinear Diffie-Hellman (BDH) assumption.

A keyword searchable attribute-based encryption scheme with attribute update for cloud storage

PubMed Central

Wang, Shangping; Zhang, Yaling

2018-01-01

Ciphertext-policy attribute-based encryption (CP-ABE) scheme is a new type of data encryption primitive, which is very suitable for data cloud storage for its fine-grained access control. Keyword-based searchable encryption scheme enables users to quickly find interesting data stored in the cloud server without revealing any information of the searched keywords. In this work, we provide a keyword searchable attribute-based encryption scheme with attribute update for cloud storage, which is a combination of attribute-based encryption scheme and keyword searchable encryption scheme. The new scheme supports the user's attribute update, especially in our new scheme when a user's attribute need to be updated, only the user's secret key related with the attribute need to be updated, while other user's secret key and the ciphertexts related with this attribute need not to be updated with the help of the cloud server. In addition, we outsource the operation with high computation cost to cloud server to reduce the user's computational burden. Moreover, our scheme is proven to be semantic security against chosen ciphertext-policy and chosen plaintext attack in the general bilinear group model. And our scheme is also proven to be semantic security against chosen keyword attack under bilinear Diffie-Hellman (BDH) assumption. PMID:29795577

Virtual Solar Observatory Distributed Query Construction

NASA Technical Reports Server (NTRS)

Gurman, J. B.; Dimitoglou, G.; Bogart, R.; Davey, A.; Hill, F.; Martens, P.

2003-01-01

Through a prototype implementation (Tian et al., this meeting) the VSO has already demonstrated the capability of unifying geographically distributed data sources following the Web Services paradigm and utilizing mechanisms such as the Simple Object Access Protocol (SOAP). So far, four participating sites (Stanford, Montana State University, National Solar Observatory and the Solar Data Analysis Center) permit Web-accessible, time-based searches that allow browse access to a number of diverse data sets. Our latest work includes the extension of the simple, time-based queries to include numerous other searchable observation parameters. For VSO users, this extended functionality enables more refined searches. For the VSO, it is a proof of concept that more complex, distributed queries can be effectively constructed and that results from heterogeneous, remote sources can be synthesized and presented to users as a single, virtual data product.

Analysis of secondary structural elements in human microRNA hairpin precursors.

PubMed

Liu, Biao; Childs-Disney, Jessica L; Znosko, Brent M; Wang, Dan; Fallahi, Mohammad; Gallo, Steven M; Disney, Matthew D

2016-03-01

MicroRNAs (miRNAs) regulate gene expression by targeting complementary mRNAs for destruction or translational repression. Aberrant expression of miRNAs has been associated with various diseases including cancer, thus making them interesting therapeutic targets. The composite of secondary structural elements that comprise miRNAs could aid the design of small molecules that modulate their function. We analyzed the secondary structural elements, or motifs, present in all human miRNA hairpin precursors and compared them to highly expressed human RNAs with known structures and other RNAs from various organisms. Amongst human miRNAs, there are 3808 are unique motifs, many residing in processing sites. Further, we identified motifs in miRNAs that are not present in other highly expressed human RNAs, desirable targets for small molecules. MiRNA motifs were incorporated into a searchable database that is freely available. We also analyzed the most frequently occurring bulges and internal loops for each RNA class and found that the smallest loops possible prevail. However, the distribution of loops and the preferred closing base pairs were unique to each class. Collectively, we have completed a broad survey of motifs found in human miRNA precursors, highly expressed human RNAs, and RNAs from other organisms. Interestingly, unique motifs were identified in human miRNA processing sites, binding to which could inhibit miRNA maturation and hence function.

Interspecies quantitative structure-activity relationships (QSARs) for eco-toxicity screening of chemicals: the role of physicochemical properties.

PubMed

Furuhama, A; Hasunuma, K; Aoki, Y

2015-01-01

In addition to molecular structure profiles, descriptors based on physicochemical properties are useful for explaining the eco-toxicities of chemicals. In a previous study we reported that a criterion based on the difference between the partition coefficient (log POW) and distribution coefficient (log D) values of chemicals enabled us to identify aromatic amines and phenols for which interspecies relationships with strong correlations could be developed for fish-daphnid and algal-daphnid toxicities. The chemicals that met the log D-based criterion were expected to have similar toxicity mechanisms (related to membrane penetration). Here, we investigated the applicability of log D-based criteria to the eco-toxicity of other kinds of chemicals, including aliphatic compounds. At pH 10, use of a log POW - log D > 0 criterion and omission of outliers resulted in the selection of more than 100 chemicals whose acute fish toxicities or algal growth inhibition toxicities were almost equal to their acute daphnid toxicities. The advantage of log D-based criteria is that they allow for simple, rapid screening and prioritizing of chemicals. However, inorganic molecules and chemicals containing certain structural elements cannot be evaluated, because calculated log D values are unavailable.

Updating a Searchable Database of Dropout Prevention Programs and Policies in Nine Low-Income Urban School Districts in the Northeast and Islands Region. REL Technical Brief. REL 2012-No. 020

ERIC Educational Resources Information Center

Myint-U, Athi; O'Donnell, Lydia; Phillips, Dawna

2012-01-01

This technical brief describes updates to a database of dropout prevention programs and policies in 2006/07 created by the Regional Education Laboratory (REL) Northeast and Islands and described in the Issues & Answers report, "Piloting a searchable database of dropout prevention programs in nine low-income urban school districts in the…

40 CFR 745.84 - Information distribution requirements.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 30 2010-07-01 2010-07-01 false Information distribution requirements. 745.84 Section 745.84 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Residential...

40 CFR 745.84 - Information distribution requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... 40 Protection of Environment 32 2013-07-01 2013-07-01 false Information distribution requirements. 745.84 Section 745.84 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Residential...

40 CFR 745.84 - Information distribution requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... 40 Protection of Environment 31 2014-07-01 2014-07-01 false Information distribution requirements. 745.84 Section 745.84 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Residential...

40 CFR 745.84 - Information distribution requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Information distribution requirements. 745.84 Section 745.84 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Residential...

40 CFR 745.84 - Information distribution requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... 40 Protection of Environment 31 2011-07-01 2011-07-01 false Information distribution requirements. 745.84 Section 745.84 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES Residential...

Toxicity challenges in environmental chemicals: Prediction of human plasma protein binding through quantitative structure-activity relationship (QSAR) models (2016 IVIVE Workshop Proceedings)

EPA Science Inventory

Physiologically based pharmacokinetic (PBPK) models bridge the gap between in vitro assays and in vivo effects by accounting for the adsorption, distribution, metabolism, and excretion of xenobiotics, which is especially useful in the assessment of human toxicity. Quantitative st...

WEB-BASED DATABASE ON RENEWAL TECHNOLOGIES ...

EPA Pesticide Factsheets

As U.S. utilities continue to shore up their aging infrastructure, renewal needs now represent over 43% of annual expenditures compared to new construction for drinking water distribution and wastewater collection systems (Underground Construction [UC], 2016). An increased understanding of renewal options will ultimately assist drinking water utilities in reducing water loss and help wastewater utilities to address infiltration and inflow issues in a cost-effective manner. It will also help to extend the service lives of both drinking water and wastewater mains. This research effort involved collecting case studies on the use of various trenchless pipeline renewal methods and providing the information in an online searchable database. The overall objective was to further support technology transfer and information sharing regarding emerging and innovative renewal technologies for water and wastewater mains. The result of this research is a Web-based, searchable database that utility personnel can use to obtain technology performance and cost data, as well as case study references. The renewal case studies include: technologies used; the conditions under which the technology was implemented; costs; lessons learned; and utility contact information. The online database also features a data mining tool for automated review of the technologies selected and cost data. Based on a review of the case study results and industry data, several findings are presented on tren

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

Harkema, J.R.

The nasal cavity is susceptible to chemically induced injury as a result of exposure to inhaled irritants. Some responses of the nasal mucosa to inhaled toxicants are species specific. These species-related differences in response may be due to variations in structural, physiologic, and biochemical factors, such as gross nasal cavity structure, distribution of luminal epithelial cell populations along the nasal airway, intranasal airflow patterns, nasal mucociliary apparatus, and nasal xenobiotic metabolism among animal species. This paper reviews the comparative anatomy and irritant-induced pathology of the nasal cavity in laboratory animals. The toxicologist, pathologist, and environmental risk assessor must have amore » good working knowledge of the similarities and differences in normal nasal structure and response to injury among species before they can select animal models for nasal toxicity studies, recognize toxicant-induced lesions in the nasal airway, and extrapolate experimental results to estimate the possible effects of an inhaled toxicant on the human nasal airway.« less

Pharmacokinetic drivers of toxicity for basic molecules: Strategy to lower pKa results in decreased tissue exposure and toxicity for a small molecule Met inhibitor

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

Diaz, Dolores, E-mail: diaz.dolores@gene.com; Ford, Kevin A.; Hartley, Dylan P.

Several toxicities are clearly driven by free drug concentrations in plasma, such as toxicities related to on-target exaggerated pharmacology or off-target pharmacological activity associated with receptors, enzymes or ion channels. However, there are examples in which organ toxicities appear to correlate better with total drug concentrations in the target tissues, rather than with free drug concentrations in plasma. Here we present a case study in which a small molecule Met inhibitor, GEN-203, with significant liver and bone marrow toxicity in preclinical species was modified with the intention of increasing the safety margin. GEN-203 is a lipophilic weak base as demonstratedmore » by its physicochemical and structural properties: high LogD (distribution coefficient) (4.3) and high measured pKa (7.45) due to the basic amine (N-ethyl-3-fluoro-4-aminopiperidine). The physicochemical properties of GEN-203 were hypothesized to drive the high distribution of this compound to tissues as evidenced by a moderately-high volume of distribution (Vd > 3 l/kg) in mouse and subsequent toxicities of the compound. Specifically, the basicity of GEN-203 was decreased through addition of a second fluorine in the 3-position of the aminopiperidine to yield GEN-890 (N-ethyl-3,3-difluoro-4-aminopiperidine), which decreased the volume of distribution of the compound in mouse (Vd = 1.0 l/kg), decreased its tissue drug concentrations and led to decreased toxicity in mice. This strategy suggests that when toxicity is driven by tissue drug concentrations, optimization of the physicochemical parameters that drive tissue distribution can result in decreased drug concentrations in tissues, resulting in lower toxicity and improved safety margins. -- Highlights: ► Lower pKa for a small molecule: reduced tissue drug levels and toxicity. ► New analysis tools to assess electrostatic effects and ionization are presented. ► Chemical and PK drivers of toxicity can be leveraged to improve safety.« less

Neuropeptide imaging on an LTQ with vMALDI source: The complete `all-in-one' peptidome analysis

NASA Astrophysics Data System (ADS)

Verhaert, Peter D.; Conaway, Maria C. Prieto; Pekar, Tonya M.; Miller, Ken

2007-02-01

Direct tissue imaging was performed on dissected insect tissue using a MALDI ion trap to visualize endogenous neuropeptides. Coupling tissue imaging to tandem MSn allows for the identification of previously known species and the ability to identify new ones by de novo sequencing, as searchable databases for insects are sparse. Direct tissue imaging is an attractive technique for the study of neuropeptides as minimal sample preparation is required prior to mass spectrometry. We successfully identified neuropeptides present in the corpora cardiaca and allata of Acheta domesticus (the house cricket). Diagnostic fragments at low m/z were used to distinguish between lipids and neuropeptides. The distribution of peptides appears to be more differentially localized than that of phospholipids, which seem to be more evenly distributed within the tissue.

40 CFR 745.326 - Renovation: State and Tribal program requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

...) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES... distribution of lead hazard information to owners and occupants of target housing and child-occupied facilities... distributing the lead hazard information to owners and occupants of housing and child-occupied facilities prior...

SBDN: an information portal on small bodies and interplanetary dust inside the Europlanet Research Infrastructure

NASA Astrophysics Data System (ADS)

Turrini, Diego; de Sanctis, Maria Cristina; Carraro, Francesco; Fonte, Sergio; Giacomini, Livia; Politi, Romolo

In the framework of the Sixth Framework Programme (FP6) for Research and Technological Development of the European Community, the Europlanet project started the Integrated and Distributed Information Service (IDIS) initiative. The goal of this initiative was to "...offer to the planetary science community a common and user-friendly access to the data and infor-mation produced by the various types of research activities: earth-based observations, space observations, modelling and theory, laboratory experiments...". Four scientific nodes, repre-sentative of a significant fraction of the scientific themes covered by planetary sciences, were created: the Interiors and Surfaces node, the Atmospheres node, the Plasma node and the Small Bodies and Dust node. The original Europlanet program evolved into the Europlanet Research Infrastructure project, funded by the Seventh Framework Programme (FP7) for Research and Technological Development, and the IDIS initiative has been renewed with the addiction of a new scientific node, the Planetary Dynamics node. Here we present the Small Bodies and Dust node (SBDN) and the services it already provides to the scientific community, i.e. a searchable database of resources related to its thematic domains, an online and searchable cat-alogue of emission lines observed in the visible spectrum of comet 153P/2002 C1 Ikeya-Zhang supplemented by a visualization facility, a set of models of the simulated evolution of comet 67P/Churyumov-Gerasimenko with a particular focus on the effects of the distribution of dust and a information system on meteors through the Virtual Meteor Observatory. We will also introduce the new services that will be implemented and made available in the course of the Europlanet Research Infrastructure project.

The Distribution of Fruit and Seed Toxicity during Development for Eleven Neotropical Trees and Vines in Central Panama

PubMed Central

Beckman, Noelle G.

2013-01-01

Secondary compounds in fruit mediate interactions with natural enemies and seed dispersers, influencing plant survival and species distributions. The functions of secondary metabolites in plant defenses have been well-studied in green tissues, but not in reproductive structures of plants. In this study, the distribution of toxicity within plants was quantified and its influence on seed survival was determined in Central Panama. To investigate patterns of allocation to chemical defenses and shifts in allocation with fruit development, I quantified variation in toxicity between immature and mature fruit and between the seed and pericarp for eleven species. Toxicity of seed and pericarp was compared to leaf toxicity for five species. Toxicity was measured as reduced hyphal growth of two fungal pathogens, Phoma sp. and Fusarium sp., and reduced survivorship of brine shrimp, Artemia franciscana, across a range of concentrations of crude extract. I used these measures of potential toxicity against generalist natural enemies to examine the effect of fruit toxicity on reductions of fruit development and seed survival by vertebrates, invertebrates, and pathogens measured for seven species in a natural enemy removal experiment. The seed or pericarp of all vertebrate- and wind-dispersed species reduced Artemia survivorship and hyphal growth of Fusarium during the immature and mature stages. Only mature fruit of two vertebrate-dispersed species reduced hyphal growth of Phoma. Predispersal seed survival increased with toxicity of immature fruit to Artemia during germination and decreased with toxicity to fungi during fruit development. This study suggests that fruit toxicity against generalist natural enemies may be common in Central Panama. These results support the hypothesis that secondary metabolites in fruit have adaptive value and are important in the evolution of fruit-frugivore interactions. PMID:23843965

Assemble: an interactive graphical tool to analyze and build RNA architectures at the 2D and 3D levels.

PubMed

Jossinet, Fabrice; Ludwig, Thomas E; Westhof, Eric

2010-08-15

Assemble is an intuitive graphical interface to analyze, manipulate and build complex 3D RNA architectures. It provides several advanced and unique features within the framework of a semi-automated modeling process that can be performed by homology and ab initio with or without electron density maps. Those include the interactive editing of a secondary structure and a searchable, embedded library of annotated tertiary structures. Assemble helps users with performing recurrent and otherwise tedious tasks in structural RNA research. Assemble is released under an open-source license (MIT license) and is freely available at http://bioinformatics.org/assemble. It is implemented in the Java language and runs on MacOSX, Linux and Windows operating systems.

Assessing deep and shallow learning methods for quantitative prediction of acute chemical toxicity.

PubMed

Liu, Ruifeng; Madore, Michael; Glover, Kyle P; Feasel, Michael G; Wallqvist, Anders

2018-05-02

Animal-based methods for assessing chemical toxicity are struggling to meet testing demands. In silico approaches, including machine-learning methods, are promising alternatives. Recently, deep neural networks (DNNs) were evaluated and reported to outperform other machine-learning methods for quantitative structure-activity relationship modeling of molecular properties. However, most of the reported performance evaluations relied on global performance metrics, such as the root mean squared error (RMSE) between the predicted and experimental values of all samples, without considering the impact of sample distribution across the activity spectrum. Here, we carried out an in-depth analysis of DNN performance for quantitative prediction of acute chemical toxicity using several datasets. We found that the overall performance of DNN models on datasets of up to 30,000 compounds was similar to that of random forest (RF) models, as measured by the RMSE and correlation coefficients between the predicted and experimental results. However, our detailed analyses demonstrated that global performance metrics are inappropriate for datasets with a highly uneven sample distribution, because they show a strong bias for the most populous compounds along the toxicity spectrum. For highly toxic compounds, DNN and RF models trained on all samples performed much worse than the global performance metrics indicated. Surprisingly, our variable nearest neighbor method, which utilizes only structurally similar compounds to make predictions, performed reasonably well, suggesting that information of close near neighbors in the training sets is a key determinant of acute toxicity predictions.

ProBiS-database: precalculated binding site similarities and local pairwise alignments of PDB structures.

PubMed

Konc, Janez; Cesnik, Tomo; Konc, Joanna Trykowska; Penca, Matej; Janežič, Dušanka

2012-02-27

ProBiS-Database is a searchable repository of precalculated local structural alignments in proteins detected by the ProBiS algorithm in the Protein Data Bank. Identification of functionally important binding regions of the protein is facilitated by structural similarity scores mapped to the query protein structure. PDB structures that have been aligned with a query protein may be rapidly retrieved from the ProBiS-Database, which is thus able to generate hypotheses concerning the roles of uncharacterized proteins. Presented with uncharacterized protein structure, ProBiS-Database can discern relationships between such a query protein and other better known proteins in the PDB. Fast access and a user-friendly graphical interface promote easy exploration of this database of over 420 million local structural alignments. The ProBiS-Database is updated weekly and is freely available online at http://probis.cmm.ki.si/database.

Method for spatially distributing a population

DOEpatents

Bright, Edward A [Knoxville, TN; Bhaduri, Budhendra L [Knoxville, TN; Coleman, Phillip R [Knoxville, TN; Dobson, Jerome E [Lawrence, KS

2007-07-24

A process for spatially distributing a population count within a geographically defined area can include the steps of logically correlating land usages apparent from a geographically defined area to geospatial features in the geographically defined area and allocating portions of the population count to regions of the geographically defined area having the land usages, according to the logical correlation. The process can also include weighing the logical correlation for determining the allocation of portions of the population count and storing the allocated portions within a searchable data store. The logically correlating step can include the step of logically correlating time-based land usages to geospatial features of the geographically defined area. The process can also include obtaining a population count for the geographically defined area, organizing the geographically defined area into a plurality of sectors, and verifying the allocated portions according to direct observation.

Bacteria use type IV pili to walk upright and detach from surfaces.

PubMed

Gibiansky, Maxsim L; Conrad, Jacinta C; Jin, Fan; Gordon, Vernita D; Motto, Dominick A; Mathewson, Margie A; Stopka, Wiktor G; Zelasko, Daria C; Shrout, Joshua D; Wong, Gerard C L

2010-10-08

Bacterial biofilms are structured multicellular communities involved in a broad range of infections. Knowing how free-swimming bacteria adapt their motility mechanisms near surfaces is crucial for understanding the transition between planktonic and biofilm phenotypes. By translating microscopy movies into searchable databases of bacterial behavior, we identified fundamental type IV pili-driven mechanisms for Pseudomonas aeruginosa surface motility involved in distinct foraging strategies. Bacteria stood upright and "walked" with trajectories optimized for two-dimensional surface exploration. Vertical orientation facilitated surface detachment and could influence biofilm morphology.

XDS-I outsourcing proxy: ensuring confidentiality while preserving interoperability.

PubMed

Ribeiro, Luís S; Viana-Ferreira, Carlos; Oliveira, José Luís; Costa, Carlos

2014-07-01

The interoperability of services and the sharing of health data have been a continuous goal for health professionals, patients, institutions, and policy makers. However, several issues have been hindering this goal, such as incompatible implementations of standards (e.g., HL7, DICOM), multiple ontologies, and security constraints. Cross-enterprise document sharing (XDS) workflows were proposed by Integrating the Healthcare Enterprise (IHE) to address current limitations in exchanging clinical data among organizations. To ensure data protection, XDS actors must be placed in trustworthy domains, which are normally inside such institutions. However, due to rapidly growing IT requirements, the outsourcing of resources in the Cloud is becoming very appealing. This paper presents a software proxy that enables the outsourcing of XDS architectural parts while preserving the interoperability, confidentiality, and searchability of clinical information. A key component in our architecture is a new searchable encryption (SE) scheme-Posterior Playfair Searchable Encryption (PPSE)-which, besides keeping the same confidentiality levels of the stored data, hides the search patterns to the adversary, bringing improvements when compared to the remaining practical state-of-the-art SE schemes.

Developing Generic Image Search Strategies for Large Astronomical Data Sets and Archives using Convolutional Neural Networks and Transfer Learning

NASA Astrophysics Data System (ADS)

Peek, Joshua E. G.; Hargis, Jonathan R.; Jones, Craig K.

2018-01-01

Astronomical instruments produce petabytes of images every year, vastly more than can be inspected by a member of the astronomical community in search of a specific population of structures. Fortunately, the sky is mostly black and source extraction algorithms have been developed to provide searchable catalogs of unconfused sources like stars and galaxies. These tools often fail for studies of more diffuse structures like the interstellar medium and unresolved stellar structures in nearby galaxies, leaving astronomers interested in observations of photodissociation regions, stellar clusters, diffuse interstellar clouds without the crucial ability to search. In this work we present a new path forward for finding structures in large data sets similar to an input structure using convolutional neural networks, transfer learning, and machine learning clustering techniques. We show applications to archival data in the Mikulski Archive for Space Telescopes (MAST).

Informing the Selection of Screening Hit Series with in Silico Absorption, Distribution, Metabolism, Excretion, and Toxicity Profiles.

PubMed

Sanders, John M; Beshore, Douglas C; Culberson, J Christopher; Fells, James I; Imbriglio, Jason E; Gunaydin, Hakan; Haidle, Andrew M; Labroli, Marc; Mattioni, Brian E; Sciammetta, Nunzio; Shipe, William D; Sheridan, Robert P; Suen, Linda M; Verras, Andreas; Walji, Abbas; Joshi, Elizabeth M; Bueters, Tjerk

2017-08-24

High-throughput screening (HTS) has enabled millions of compounds to be assessed for biological activity, but challenges remain in the prioritization of hit series. While biological, absorption, distribution, metabolism, excretion, and toxicity (ADMET), purity, and structural data are routinely used to select chemical matter for further follow-up, the scarcity of historical ADMET data for screening hits limits our understanding of early hit compounds. Herein, we describe a process that utilizes a battery of in-house quantitative structure-activity relationship (QSAR) models to generate in silico ADMET profiles for hit series to enable more complete characterizations of HTS chemical matter. These profiles allow teams to quickly assess hit series for desirable ADMET properties or suspected liabilities that may require significant optimization. Accordingly, these in silico data can direct ADMET experimentation and profoundly impact the progression of hit series. Several prospective examples are presented to substantiate the value of this approach.

Tetrodotoxin: Chemistry, Toxicity, Source, Distribution and Detection

PubMed Central

Bane, Vaishali; Lehane, Mary; Dikshit, Madhurima; O’Riordan, Alan; Furey, Ambrose

2014-01-01

Tetrodotoxin (TTX) is a naturally occurring toxin that has been responsible for human intoxications and fatalities. Its usual route of toxicity is via the ingestion of contaminated puffer fish which are a culinary delicacy, especially in Japan. TTX was believed to be confined to regions of South East Asia, but recent studies have demonstrated that the toxin has spread to regions in the Pacific and the Mediterranean. There is no known antidote to TTX which is a powerful sodium channel inhibitor. This review aims to collect pertinent information available to date on TTX and its analogues with a special emphasis on the structure, aetiology, distribution, effects and the analytical methods employed for its detection. PMID:24566728

Determination of ortho-cresyl phosphate isomers of tricresyl phosphate used in aircraft turbine engine oils by gas chromatography and mass spectrometry.

PubMed

De Nola, G; Kibby, J; Mazurek, W

2008-07-25

Tricresyl phosphate (TCP) is used as an anti-wear additive in aircraft turbine engine oil. Concerns about its toxicity are largely based on the tri-o-cresyl phosphate isomer content. However, the presence of other and more toxic isomers has been previously suggested. In this work, the structural isomers of TCP have been determined by two methods (experimental and semi-theoretical). First, the TCP isomers were separated by gas chromatography (GC) and identified by mass spectrometry (MS). Second, after base cleavage of TCP, GC was used to quantify the cresol precursors. These results were used to calculate the TCP isomer distribution based on the assumption of a statistical distribution of the TCP isomers. The results from the two determinations showed reasonable agreement for three of the four oils studied. The o-cresyl isomers were found to be present almost exclusively as the more toxic mono-o-cresyl isomers in the concentration range 13-150 mg/L. The ability to analyse for the mono-o-cresyl isomers allows the toxicity of TCP to be based on the latter isomers rather than on the less toxic tri-o-cresyl phosphate isomer.

Two Delphinium ramosum chemotypes, their biogeographical distribution and potential toxicity

USDA-ARS?s Scientific Manuscript database

Larkspurs (Delphinium spp.) are poisonous plants found on rangelands throughout Western North America. Two main structural groups of norditerpene alkaloids, the N-(methylsuccinimido) anthranoyllycoctonine type (MSAL-type) and the non-MSAL type, are responsible for larkspur-induced poisoning. Informa...

The RCSB protein data bank: integrative view of protein, gene and 3D structural information

PubMed Central

Rose, Peter W.; Prlić, Andreas; Altunkaya, Ali; Bi, Chunxiao; Bradley, Anthony R.; Christie, Cole H.; Costanzo, Luigi Di; Duarte, Jose M.; Dutta, Shuchismita; Feng, Zukang; Green, Rachel Kramer; Goodsell, David S.; Hudson, Brian; Kalro, Tara; Lowe, Robert; Peisach, Ezra; Randle, Christopher; Rose, Alexander S.; Shao, Chenghua; Tao, Yi-Ping; Valasatava, Yana; Voigt, Maria; Westbrook, John D.; Woo, Jesse; Yang, Huangwang; Young, Jasmine Y.; Zardecki, Christine; Berman, Helen M.; Burley, Stephen K.

2017-01-01

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB PDB, http://rcsb.org), the US data center for the global PDB archive, makes PDB data freely available to all users, from structural biologists to computational biologists and beyond. New tools and resources have been added to the RCSB PDB web portal in support of a ‘Structural View of Biology.’ Recent developments have improved the User experience, including the high-speed NGL Viewer that provides 3D molecular visualization in any web browser, improved support for data file download and enhanced organization of website pages for query, reporting and individual structure exploration. Structure validation information is now visible for all archival entries. PDB data have been integrated with external biological resources, including chromosomal position within the human genome; protein modifications; and metabolic pathways. PDB-101 educational materials have been reorganized into a searchable website and expanded to include new features such as the Geis Digital Archive. PMID:27794042

A User-Friendly, Keyword-Searchable Database of Geoscientific References Through 2007 for Afghanistan

USGS Publications Warehouse

Eppinger, Robert G.; Sipeki, Julianna; Scofield, M.L. Sco

2008-01-01

This report includes a document and accompanying Microsoft Access 2003 database of geoscientific references for the country of Afghanistan. The reference compilation is part of a larger joint study of Afghanistan?s energy, mineral, and water resources, and geologic hazards currently underway by the U.S. Geological Survey, the British Geological Survey, and the Afghanistan Geological Survey. The database includes both published (n = 2,489) and unpublished (n = 176) references compiled through calendar year 2007. The references comprise two separate tables in the Access database. The reference database includes a user-friendly, keyword-searchable interface and only minimum knowledge of the use of Microsoft Access is required.

A Web-based searchable system to confirm magnetic resonance compatibility of implantable medical devices in Japan: a preliminary study.

PubMed

Fujiwara, Yasuhiro; Fujioka, Hitoshi; Watanabe, Tomoko; Sekiguchi, Maiko; Murakami, Ryuji

2017-09-01

Confirmation of the magnetic resonance (MR) compatibility of implanted medical devices (IMDs) is mandatory before conducting magnetic resonance imaging (MRI) examinations. In Japan, few such confirmation methods are in use, and they are time-consuming. This study aimed to develop a Web-based searchable MR safety information system to confirm IMD compatibility and to evaluate the usefulness of the system. First, MR safety information for intravascular stents and stent grafts sold in Japan was gathered by interviewing 20 manufacturers. These IMDs were categorized based on the descriptions available on medical package inserts as: "MR Safe," "MR Conditional," "MR Unsafe," "Unknown," and "No Medical Package Insert Available". An MR safety information database for implants was created based on previously proposed item lists. Finally, a Web-based searchable system was developed using this database. A questionnaire was given to health-care personnel in Japan to evaluate the usefulness of this system. Seventy-nine datasets were collected using information provided by 12 manufacturers and by investigating the medical packaging of the IMDs. Although the datasets must be updated by collecting data from other manufacturers, this system facilitates the easy and rapid acquisition of MR safety information for IMDs, thereby improving the safety of MRI examinations.

Assessment of medication adherence app features, functionality, and health literacy level and the creation of a searchable Web-based adherence app resource for health care professionals and patients.

PubMed

Heldenbrand, Seth; Martin, Bradley C; Gubbins, Paul O; Hadden, Kristie; Renna, Catherine; Shilling, Rebecca; Dayer, Lindsey

2016-01-01

To assess the features and level of health literacy (HL) of available medication adherence apps and to create a searchable website to assist health care providers (HCP) and patients identify quality adherence apps. Medication nonadherence continues to be a significant problem and leads to poor health outcomes and avoidable health care expense. The average adherence rate for chronic medications, regardless of disease state, is approximately 50% leaving significant room for improvement. Smartphone adherence apps are a novel resource to address medication nonadherence. With widespread smartphone use and the growing number of adherence apps, both HCP and patients should be able to identify quality adherence apps to maximize potential benefits. Assess the features, functionality and level of HL of available adherence apps and create a searchable website to help both HCP and patients identify quality adherence apps. Online marketplaces (iTunes, Google Play, Blackberry) were searched in June of 2014 to identify available adherence apps. Online descriptions were recorded and scored based on 28 author-identified features across 4 domains. The 100 highest-scoring apps were user-tested with a standardized regimen to evaluate their functionality and level of HL. 461 adherence apps were identified. 367 unique apps were evaluated after removing "Lite/Trial" versions. The median initial score based on descriptions was 15 (max of 68; range: 3 to 47). Only 77 apps of the top 100 highest-scoring apps completed user-testing and HL evaluations. The median overall user-testing score was 30 (max of 73; range: 16 to 55). App design, functionality, and level of HL varies widely among adherence apps. While no app is perfect, several apps scored highly across all domains. The website www.medappfinder.com is a searchable tool that helps HCP and patients identify quality apps in a crowded marketplace. Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

The U.S. Dairy Forage Research Center (USDFRC) Condensed Tannin NMR Database.

PubMed

Zeller, Wayne E; Schatz, Paul F

2017-06-28

This Perspective describes a solution-state NMR database for flavan-3-ol monomers and condensed tannin dimers through tetramers obtained from the literature to 2015, containing data searchable by structure, molecular formula, degrees of polymerization, and 1 H and 13 C chemical shifts of the condensed tannins. Citations for all literature references are provided and should serve as valuable resource for scientists working in the field of condensed tannin research. The database will be periodically updated as additional information becomes available, typically on a yearly basis and is available for use, free of charge, from the U.S. Dairy Forage Research Center (USDFRC) Website.

Analysis of quantitative data obtained from toxicity studies showing non-normal distribution.

PubMed

Kobayashi, Katsumi

2005-05-01

The data obtained from toxicity studies are examined for homogeneity of variance, but, usually, they are not examined for normal distribution. In this study I examined the measured items of a carcinogenicity/chronic toxicity study with rats for both homogeneity of variance and normal distribution. It was observed that a lot of hematology and biochemistry items showed non-normal distribution. For testing normal distribution of the data obtained from toxicity studies, the data of the concurrent control group may be examined, and for the data that show a non-normal distribution, non-parametric tests with robustness may be applied.

Using machine learning and quantum chemistry descriptors to predict the toxicity of ionic liquids.

PubMed

Cao, Lingdi; Zhu, Peng; Zhao, Yongsheng; Zhao, Jihong

2018-06-15

Large-scale application of ionic liquids (ILs) hinges on the advancement of designable and eco-friendly nature. Research of the potential toxicity of ILs towards different organisms and trophic levels is insufficient. Quantitative structure-activity relationships (QSAR) model is applied to evaluate the toxicity of ILs towards the leukemia rat cell line (ICP-81). The structures of 57 cations and 21 anions were optimized by quantum chemistry. The electrostatic potential surface area (S EP ) and charge distribution area (S σ-profile ) descriptors are calculated and used to predict the toxicity of ILs. The performance and predictive aptitude of extreme learning machine (ELM) model are analyzed and compared with those of multiple linear regression (MLR) and support vector machine (SVM) models. The highest R 2 and the lowest AARD% and RMSE of the training set, test set and total set for the ELM are observed, which validates the superior performance of the ELM than that of obtained by the MLR and SVM. The applicability domain of the model is assessed by the Williams plot. Copyright © 2018 Elsevier B.V. All rights reserved.

Augmenting aquatic species sensitivity distributions with interspecies toxicity estimation models

EPA Science Inventory

Species sensitivity distributions (SSD) are cumulative distribution functions of species toxicity values. The SSD approach is increasingly being used in ecological risk assessment, but is often limited by available toxicity data necessary for diverse species representation. In ...

Concentration rather than dose defines the local brain toxicity of agents that are effectively distributed by convection-enhanced delivery.

PubMed

Zhang, Rong; Saito, Ryuta; Mano, Yui; Kanamori, Masayuki; Sonoda, Yukihiko; Kumabe, Toshihiro; Tominaga, Teiji

2014-01-30

Convection-enhanced delivery (CED) has been developed as a potentially effective drug-delivery strategy into the central nervous system. In contrast to systemic intravenous administration, local delivery achieves high concentration and prolonged retention in the local tissue, with increased chance of local toxicity, especially with toxic agents such as chemotherapeutic agents. Therefore, the factors that affect local toxicity should be extensively studied. With the assumption that concentration-oriented evaluation of toxicity is important for local CED, we evaluated the appearance of local toxicity among different agents after delivery with CED and studied if it is dose dependent or concentration dependent. Local toxicity profile of chemotherapeutic agents delivered via CED indicates BCNU was dose-dependent, whereas that of ACNU was concentration-dependent. On the other hand, local toxicity for doxorubicin, which is not distributed effectively by CED, was dose-dependent. Local toxicity for PLD, which is extensively distributed by CED, was concentration-dependent. Traditional evaluation of drug induced toxicity was dose-oriented. This is true for systemic intravascular delivery. However, with local CED, toxicity of several drugs exacerbated in concentration-dependent manner. From our study, local toxicity of drugs that are likely to distribute effectively tended to be concentration-dependent. Concentration rather than dose may be more important for the toxicity of agents that are effectively distributed by CED. Concentration-oriented evaluation of toxicity is more important for CED. Copyright © 2013 Elsevier B.V. All rights reserved.

A geometric model of mortality and crop protection for insects feeding on discrete toxicant deposits.

PubMed

Ebert, Timothy; Derksen, Richard

2004-04-01

Current theory governing the biological effectiveness of toxicants stresses the dose-response relationship and focuses on uniform toxicant distributions in the insect's environment. However, toxicants are seldom uniformly dispersed under field conditions. Toxicant distribution affects bioavailability, but the mechanics of such interactions is not well documented. We present a geometric model of the interactions between insects and heterogeneously distributed toxicants. From the model, we conclude the following: 1) There is an optimal droplet size, and droplets both smaller and larger than this optimum will decrease efficacy. 2) There is an ideal droplet distribution. Droplets should be spaced based on two criteria: calculate the allowable damage, double this quantity, and one lethal deposit should be placed in this area; and define the quantity of leaf the larva could eat before the toxicant decays below the lethal level and place one lethal deposit within this area. 3) Distributions of toxicant where deposits are sublethal will often be ineffective, but the application is wasteful if deposits contain more than a lethal dose. 4) Insect behavior both as individuals and collectively influences the level of crop production provided by an application. This conclusion has implications for both crop protection and natural plant-insect interactions. The effective utilization of new more environmentally sensitive toxicants may depend on how well we understand how heterogeneous toxicant distributions interact with insect behavior to determine the biological outcome.

Development of Species Sensitivity Distributions for Wildlife Using Interspecies Toxicity Correlation Models

EPA Science Inventory

Species sensitivity distributions (SSD) are cumulative distributions of chemical toxicity of multiple species and have had limited application in wildlife risk assessment because of relatively small datasets of wildlife toxicity values. Interspecies correlation estimation (ICE) m...

Questions to Ask Your Doctor

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

40 CFR 745.326 - Renovation: State and Tribal program requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

...) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES... distribution of lead hazard information to owners and occupants of target housing and child-occupied facilities... sampling to be performed by a certified lead-based paint inspector or risk assessor. (ii) Procedures and...

40 CFR 745.326 - Renovation: State and Tribal program requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

...) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES... distribution of lead hazard information to owners and occupants of target housing and child-occupied facilities... sampling to be performed by a certified lead-based paint inspector or risk assessor. (ii) Procedures and...

40 CFR 745.326 - Renovation: State and Tribal program requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

...) TOXIC SUBSTANCES CONTROL ACT LEAD-BASED PAINT POISONING PREVENTION IN CERTAIN RESIDENTIAL STRUCTURES... distribution of lead hazard information to owners and occupants of target housing and child-occupied facilities... sampling to be performed by a certified lead-based paint inspector or risk assessor. (ii) Procedures and...

The Fermi Science Support Center Data Servers and Archive

NASA Astrophysics Data System (ADS)

Reustle, Alexander; Fermi Science Support Center

2018-01-01

The Fermi Science Support Center (FSSC) provides the scientific community with access to Fermi data and other products. The Gamma-Ray Burst Monitor (GBM) data is stored at NASA's High Energy Astrophysics Science Archive Research Center (HEASARC) and is accessible through their searchable Browse web interface. The Large Area Telescope (LAT) data is distributed through a custom FSSC interface where users can request all photons detected from a region on the sky over a specified time and energy range. Through its website the FSSC also provides planning and scheduling products, such as long and short term observing timelines, spacecraft position and attitude histories, and exposure maps. We present an overview of the different data products provided by the FSSC, how they can be accessed, and statistics on the archive usage since launch.

Comparison of Species Sensitivity Distributions Derived from Interspecies Correlation Models to Distributions used to Derive Water Quality Criteria

EPA Science Inventory

Species sensitivity distributions (SSD) require a large number of measured toxicity values to define a chemical’s toxicity to multiple species. This investigation comprehensively evaluated the accuracy of SSDs generated from toxicity values predicted from interspecies correlation...

Syringomyelia

MedlinePlus

... is the most reliable way to diagnose syringomyelia. Computer-generated radio waves and a powerful magnetic field ... a searchable database of current and past research projects supported by NIH and other federal agencies. RePORTER ...

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

The Analysis of Search Results for the Clarification and Identification of Technology Emergence (AR-CITE) computer code examines a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e. scholarly publications and citation, world patents, news archives, and on-line mapping networks) are assembled to become one collective networkmore » (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the subject domain to be clarified and identified.« less

MEPD: a Medaka gene expression pattern database

PubMed Central

Henrich, Thorsten; Ramialison, Mirana; Quiring, Rebecca; Wittbrodt, Beate; Furutani-Seiki, Makoto; Wittbrodt, Joachim; Kondoh, Hisato

2003-01-01

The Medaka Expression Pattern Database (MEPD) stores and integrates information of gene expression during embryonic development of the small freshwater fish Medaka (Oryzias latipes). Expression patterns of genes identified by ESTs are documented by images and by descriptions through parameters such as staining intensity, category and comments and through a comprehensive, hierarchically organized dictionary of anatomical terms. Sequences of the ESTs are available and searchable through BLAST. ESTs in the database are clustered upon entry and have been blasted against public data-bases. The BLAST results are updated regularly, stored within the database and searchable. The MEPD is a project within the Medaka Genome Initiative (MGI) and entries will be interconnected to integrated genomic map databases. MEPD is accessible through the WWW at http://medaka.dsp.jst.go.jp/MEPD. PMID:12519950

Efficient secure-channel free public key encryption with keyword search for EMRs in cloud storage.

PubMed

Guo, Lifeng; Yau, Wei-Chuen

2015-02-01

Searchable encryption is an important cryptographic primitive that enables privacy-preserving keyword search on encrypted electronic medical records (EMRs) in cloud storage. Efficiency of such searchable encryption in a medical cloud storage system is very crucial as it involves client platforms such as smartphones or tablets that only have constrained computing power and resources. In this paper, we propose an efficient secure-channel free public key encryption with keyword search (SCF-PEKS) scheme that is proven secure in the standard model. We show that our SCF-PEKS scheme is not only secure against chosen keyword and ciphertext attacks (IND-SCF-CKCA), but also secure against keyword guessing attacks (IND-KGA). Furthermore, our proposed scheme is more efficient than other recent SCF-PEKS schemes in the literature.

Reduced Toxicity High Performance Monopropellant

DTIC Science & Technology

2011-09-01

M315E Distribution A: Approved for public release; distribution unlimited AF - M315E Desirable Properties Characteristic Objective D it *I 3450 N /L...required AF M315E d- excee s SOTA monopropellant (45%) and bipropellant (8%) Next generation exceeds SOTA monopropellant (66%) and bipropellant (23...inert mass fraction Distribution A: Approved for public release; distribution unlimited Toxicity Assessment of AF - M315E Toxicity Testing Results

GIS Modeling of Air Toxics Releases from TRI-Reporting and Non-TRI-Reporting Facilities: Impacts for Environmental Justice

PubMed Central

Dolinoy, Dana C.; Miranda, Marie Lynn

2004-01-01

The Toxics Release Inventory (TRI) requires facilities with 10 or more full-time employees that process > 25,000 pounds in aggregate or use > 10,000 pounds of any one TRI chemical to report releases annually. However, little is known about releases from non-TRI-reporting facilities, nor has attention been given to the very localized equity impacts associated with air toxics releases. Using geographic information systems and industrial source complex dispersion modeling, we developed methods for characterizing air releases from TRI-reporting as well as non-TRI-reporting facilities at four levels of geographic resolution. We characterized the spatial distribution and concentration of air releases from one representative industry in Durham County, North Carolina (USA). Inclusive modeling of all facilities rather than modeling of TRI sites alone significantly alters the magnitude and spatial distribution of modeled air concentrations. Modeling exposure receptors at more refined levels of geographic resolution reveals localized, neighborhood-level exposure hot spots that are not apparent at coarser geographic scales. Multivariate analysis indicates that inclusive facility modeling at fine levels of geographic resolution reveals exposure disparities by income and race. These new methods significantly enhance the ability to model air toxics, perform equity analysis, and clarify conflicts in the literature regarding environmental justice findings. This work has substantial implications for how to structure TRI reporting requirements, as well as methods and types of analysis that will successfully elucidate the spatial distribution of exposure potentials across geographic, income, and racial lines. PMID:15579419

DFT based vibrational spectroscopic investigations and biological activity of toxic material monocrotophos

NASA Astrophysics Data System (ADS)

Nimmi, D. E.; Sam, S. P. Chandhini; Praveen, S. G.; Binoy, J.

2018-05-01

Many organophosphate compounds exhibiting toxicity are widely used as pesticides and insecticides whose structural features can be explained excellently using geometric simulation using density functional theory and vibrational spectrum. In this work, the molecular structural parameters and vibrational frequencies of the fundamental modes of Monocrotophoshave been obtained using Density functional theory (DFT), using B3LYP functional with 6-311++G(d, p) basis sets and the detailed vibrational analysis of FT-IR and FT-Ramanspectral bands have been carried out using potential energy distribution (PED). The deviation from the resonance structure of phosphate group due to `bridging of oxygen' and π-resonance of amides has been investigated based on the spectral and geometric data. The molecular docking simulation of Monocrotophos with BSA and DNA has been performed to find the mode of binding and the interactions with BSA has been investigated with UV-Visible spectroscopic method, to assess the strength of binding.

Transitioning Newborns from NICU to Home: Family Information Packet

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Next Steps After Your Diagnosis: Finding Information and Support

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Blood Thinner Pills: Your Guide to Using Them Safely

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Question Builder: Be Prepared for Your Next Medical Appointment

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

Automated Content Detection for Cassini Images

NASA Astrophysics Data System (ADS)

Stanboli, A.; Bue, B.; Wagstaff, K.; Altinok, A.

2017-06-01

NASA missions generate numerous images ever organized in increasingly large archives. Image archives are currently not searchable by image content. We present an automated content detection prototype that can enable content search.

Systematic analysis of snake neurotoxins' functional classification using a data warehousing approach.

PubMed

Siew, Joyce Phui Yee; Khan, Asif M; Tan, Paul T J; Koh, Judice L Y; Seah, Seng Hong; Koo, Chuay Yeng; Chai, Siaw Ching; Armugam, Arunmozhiarasi; Brusic, Vladimir; Jeyaseelan, Kandiah

2004-12-12

Sequence annotations, functional and structural data on snake venom neurotoxins (svNTXs) are scattered across multiple databases and literature sources. Sequence annotations and structural data are available in the public molecular databases, while functional data are almost exclusively available in the published articles. There is a need for a specialized svNTXs database that contains NTX entries, which are organized, well annotated and classified in a systematic manner. We have systematically analyzed svNTXs and classified them using structure-function groups based on their structural, functional and phylogenetic properties. Using conserved motifs in each phylogenetic group, we built an intelligent module for the prediction of structural and functional properties of unknown NTXs. We also developed an annotation tool to aid the functional prediction of newly identified NTXs as an additional resource for the venom research community. We created a searchable online database of NTX proteins sequences (http://research.i2r.a-star.edu.sg/Templar/DB/snake_neurotoxin). This database can also be found under Swiss-Prot Toxin Annotation Project website (http://www.expasy.org/sprot/).

Be More Involved in Your Health Care: Tips for Patients

MedlinePlus

... Scientific Peer Review Award Process Post-Award Grant Management AHRQ Grantee Profiles Getting Recognition for Your AHRQ-Funded Study Contracts Project Research Online Database (PROD) Searchable database of AHRQ ...

RadNet Databases and Reports

EPA Pesticide Factsheets

EPA’s RadNet data are available for viewing in a searchable database or as PDF reports. Historical and current RadNet monitoring data are used to estimate long-term trends in environmental radiation levels.

Science Inventory | US EPA

EPA Pesticide Factsheets

The Science Inventory is a searchable database of research products primarily from EPA's Office of Research and Development. Science Inventory records provide descriptions of the product, contact information, and links to available printed material or websites.

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

Abercrombie, Robert K; Udoeyop, Akaninyene W; Schlicher, Bob G

This work examines a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, patents, news archives, andmore » online mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain we investigated.« less

SABER: The Searchable Annotated Bibliography of Education Research in Astronomy

NASA Astrophysics Data System (ADS)

Bruning, David; Bailey, Janelle M.; Brissenden, Gina

Starting a new research project can be a challenge, but especially so in education research because the literature is scattered throughout many journals. Relevant astronomy education research may be in psychology journals, science education journals, physics education journals, or even in science journals. Tracking the vast realm of literature is difficult, especially because libraries frequently do not subscribe to many of the relevant journals and abstracting services. The Searchable Annotated Bibliography of Education Research (SABER) is an online resource that was started to service the needs of the astronomy education community, specifically to reduce this "scatter" by compiling an annotated bibliography of education research articles in one electronic location. Although SABER started in 2001, the database has a new URL—http://astronom- y.uwp.edu/saber/—and has recently undergone a major update.

Boron Toxicity Causes Multiple Effects on Malus domestica Pollen Tube Growth.

PubMed

Fang, Kefeng; Zhang, Weiwei; Xing, Yu; Zhang, Qing; Yang, Liu; Cao, Qingqin; Qin, Ling

2016-01-01

Boron is an important micronutrient for plants. However, boron is also toxic to cells at high concentrations, although the mechanism of this toxicity is not known. This study aimed to evaluate the effect of boron toxicity on Malus domestica pollen tube growth and its possible regulatory pathway. Our results showed that a high concentration of boron inhibited pollen germination and tube growth and led to the morphological abnormality of pollen tubes. Fluorescent labeling coupled with a scanning ion-selective electrode technique detected that boron toxicity could decrease [Ca(2+)]c and induce the disappearance of the [Ca(2+)]c gradient, which are critical for pollen tube polar growth. Actin filaments were therefore altered by boron toxicity. Immuno-localization and fluorescence labeling, together with fourier-transform infrared analysis, suggested that boron toxicity influenced the accumulation and distribution of callose, de-esterified pectins, esterified pectins, and arabinogalactan proteins in pollen tubes. All of the above results provide new insights into the regulatory role of boron in pollen tube development. In summary, boron likely plays a structural and regulatory role in relation to [Ca(2+)]c, actin cytoskeleton and cell wall components and thus regulates Malus domestica pollen germination and tube polar growth.

Boron Toxicity Causes Multiple Effects on Malus domestica Pollen Tube Growth

PubMed Central

Fang, Kefeng; Zhang, Weiwei; Xing, Yu; Zhang, Qing; Yang, Liu; Cao, Qingqin; Qin, Ling

2016-01-01

Boron is an important micronutrient for plants. However, boron is also toxic to cells at high concentrations, although the mechanism of this toxicity is not known. This study aimed to evaluate the effect of boron toxicity on Malus domestica pollen tube growth and its possible regulatory pathway. Our results showed that a high concentration of boron inhibited pollen germination and tube growth and led to the morphological abnormality of pollen tubes. Fluorescent labeling coupled with a scanning ion-selective electrode technique detected that boron toxicity could decrease [Ca2+]c and induce the disappearance of the [Ca2+]c gradient, which are critical for pollen tube polar growth. Actin filaments were therefore altered by boron toxicity. Immuno-localization and fluorescence labeling, together with fourier-transform infrared analysis, suggested that boron toxicity influenced the accumulation and distribution of callose, de-esterified pectins, esterified pectins, and arabinogalactan proteins in pollen tubes. All of the above results provide new insights into the regulatory role of boron in pollen tube development. In summary, boron likely plays a structural and regulatory role in relation to [Ca2+]c, actin cytoskeleton and cell wall components and thus regulates Malus domestica pollen germination and tube polar growth. PMID:26955377

Tidal river sediments in the Washington, D.C. area. 111 Biological effects associated with sediment contamination

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

Schlekat, C.E.; McGee, B.L.; Boward, D.M.

1994-06-01

Sediment toxicity and benthic marcroinvertebrate community structure were measured as one component of a study conceived to determine the distribution and effect of sediment contamination in tidal freshwater portions of the Potomac and Anacostia rivers in the Washington, D.C., area. Samples were collected at 15 sites. Analyses included a partial life cycle (28 d) whole sediment test using the amphipod Hyalella azteca (Talitridae) and an assessment of benthic community structure. Survival and growth (as estimated by amphipod length) were experimental endpoints for the toxicity test. Significant mortality was observed in 5 to 10 sites in the lower Anacostia River basinmore » and at the main channel Potomac River site. Sublethal toxicity, as measured by inhibition of amphipod growth, was not observed. Toxicity test results were in general agreement with synoptically measured sediment contaminant concentrations. Porewater total ammonia (NH{sub 3} + NH{sub 4}{sup +}) appears to be responsible for the toxicity of sediments from the Potomac River, while correlation analysis and simultaneously extracted metals: acid volatile sulfide (SEM:AVA) results suggest that the toxicity associated with Anacostia River sediments was due to organic compounds. Twenty-eight macroinvertebrate taxa were identified among all sites, with richness varying from 5 to 17 taxa per site. Groups of benthic assemblages identified by group-average cluster analysis exhibited variable agreement with sediment chemical and sediment toxicity results. Integration of toxicological, chemical, and ecological components suggests that adverse environmental effects manifest in lower Anacostia River benthos result from chemical contamination of sediment. 37 refs., 2 figs., 7 tabs.« less

Predictive ecotoxicity of MoA 1 of organic chemicals using in silico approaches.

PubMed

de Morais E Silva, Luana; Alves, Mateus Feitosa; Scotti, Luciana; Lopes, Wilton Silva; Scotti, Marcus Tullius

2018-05-30

Persistent organic products are compounds used for various purposes, such as personal care products, surfactants, colorants, industrial additives, food, pesticides and pharmaceuticals. These substances are constantly introduced into the environment and many of these pollutants are difficult to degrade. Toxic compounds classified as MoA 1 (Mode of Action 1) are low toxicity compounds that comprise nonreactive chemicals. In silico methods such as Quantitative Structure-Activity Relationships (QSARs) have been used to develop important models for prediction in several areas of science, as well as aquatic toxicity studies. The aim of the present study was to build a QSAR model-based set of theoretical Volsurf molecular descriptors using the fish acute toxicity values of compounds defined as MoA 1 to identify the molecular properties related to this mechanism. The selected Partial Least Squares (PLS) results based on the values of cross-validation coefficients of determination (Q cv 2 ) show the following values: Q cv 2 = 0.793, coefficient of determination (R 2 ) = 0.823, explained variance in external prediction (Q ext 2 ) = 0.87. From the selected descriptors, not only the hydrophobicity is related to the toxicity as already mentioned in previously published studies but other physicochemical properties combined contribute to the activity of these compounds. The symmetric distribution of the hydrophobic moieties in the structure of the compounds as well as the shape, as branched chains, are important features that are related to the toxicity. This information from the model can be useful in predicting so as to minimize the toxicity of organic compounds. Copyright © 2018. Published by Elsevier Inc.

Structural Fingerprinting of Nanocrystals in the Transmission Electron Microscope

NASA Astrophysics Data System (ADS)

Rouvimov, Sergei; Plachinda, Pavel; Moeck, Peter

2010-03-01

Three novel strategies for the structurally identification of nanocrystals in a transmission electron microscope are presented. Either a single high-resolution transmission electron microscopy image [1] or a single precession electron diffractogram (PED) [2] may be employed. PEDs from fine-grained crystal powders may also be utilized. Automation of the former two strategies is in progress and shall lead to statistically significant results on ensembles of nanocrystals. Open-access databases such as the Crystallography Open Database which provides more than 81,500 crystal structure data sets [3] or its mainly inorganic and educational subsets [4] may be utilized. [1] http://www.scientificjournals.org/journals 2007/j/of/dissertation.htm [2] P. Moeck and S. Rouvimov, in: {Drugs and the Pharmaceutical Sciences}, Vol. 191, 2009, 270-313 [3] http://cod.ibt.lt, http://www.crystallography.net, http://cod.ensicaen.fr, http://nanocrystallography.org, http://nanocrystallography.net, http://journals.iucr.org/j/issues/2009/04/00/kk5039/kk5039.pdf [4] http://nanocrystallography.research.pdx.edu/CIF-searchable

MPEG-7: standard metadata for multimedia content

NASA Astrophysics Data System (ADS)

Chang, Wo

2005-08-01

The eXtensible Markup Language (XML) metadata technology of describing media contents has emerged as a dominant mode of making media searchable both for human and machine consumptions. To realize this premise, many online Web applications are pushing this concept to its fullest potential. However, a good metadata model does require a robust standardization effort so that the metadata content and its structure can reach its maximum usage between various applications. An effective media content description technology should also use standard metadata structures especially when dealing with various multimedia contents. A new metadata technology called MPEG-7 content description has merged from the ISO MPEG standards body with the charter of defining standard metadata to describe audiovisual content. This paper will give an overview of MPEG-7 technology and what impact it can bring forth to the next generation of multimedia indexing and retrieval applications.

KEGG orthology-based annotation of the predicted proteome of Acropora digitifera: ZoophyteBase - an open access and searchable database of a coral genome

PubMed Central

2013-01-01

Background Contemporary coral reef research has firmly established that a genomic approach is urgently needed to better understand the effects of anthropogenic environmental stress and global climate change on coral holobiont interactions. Here we present KEGG orthology-based annotation of the complete genome sequence of the scleractinian coral Acropora digitifera and provide the first comprehensive view of the genome of a reef-building coral by applying advanced bioinformatics. Description Sequences from the KEGG database of protein function were used to construct hidden Markov models. These models were used to search the predicted proteome of A. digitifera to establish complete genomic annotation. The annotated dataset is published in ZoophyteBase, an open access format with different options for searching the data. A particularly useful feature is the ability to use a Google-like search engine that links query words to protein attributes. We present features of the annotation that underpin the molecular structure of key processes of coral physiology that include (1) regulatory proteins of symbiosis, (2) planula and early developmental proteins, (3) neural messengers, receptors and sensory proteins, (4) calcification and Ca2+-signalling proteins, (5) plant-derived proteins, (6) proteins of nitrogen metabolism, (7) DNA repair proteins, (8) stress response proteins, (9) antioxidant and redox-protective proteins, (10) proteins of cellular apoptosis, (11) microbial symbioses and pathogenicity proteins, (12) proteins of viral pathogenicity, (13) toxins and venom, (14) proteins of the chemical defensome and (15) coral epigenetics. Conclusions We advocate that providing annotation in an open-access searchable database available to the public domain will give an unprecedented foundation to interrogate the fundamental molecular structure and interactions of coral symbiosis and allow critical questions to be addressed at the genomic level based on combined aspects of evolutionary, developmental, metabolic, and environmental perspectives. PMID:23889801

Comparison of in silico models for prediction of mutagenicity.

PubMed

Bakhtyari, Nazanin G; Raitano, Giuseppa; Benfenati, Emilio; Martin, Todd; Young, Douglas

2013-01-01

Using a dataset with more than 6000 compounds, the performance of eight quantitative structure activity relationships (QSAR) models was evaluated: ACD/Tox Suite, Absorption, Distribution, Metabolism, Elimination, and Toxicity of chemical substances (ADMET) predictor, Derek, Toxicity Estimation Software Tool (T.E.S.T.), TOxicity Prediction by Komputer Assisted Technology (TOPKAT), Toxtree, CEASAR, and SARpy (SAR in python). In general, the results showed a high level of performance. To have a realistic estimate of the predictive ability, the results for chemicals inside and outside the training set for each model were considered. The effect of applicability domain tools (when available) on the prediction accuracy was also evaluated. The predictive tools included QSAR models, knowledge-based systems, and a combination of both methods. Models based on statistical QSAR methods gave better results.

76 FR 79225 - 2002 Reopened-Previously Denied Determinations; Notice of Negative Determinations on...

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2011-12-21

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American Academy of Forensic Sciences

MedlinePlus

... Academy News PDF Library Proceedings Journal of Forensic Sciences Information for Authors Searchable Index Contact Information Forensic Links ... Dale Stewart Award 2018 Annual Scientific Meeting Registration ... in Forensic Science … Now What? Young Forensic Scientists Forum (YFSF) Annual ...

A few scenarios still do not fit all

NASA Astrophysics Data System (ADS)

Schweizer, Vanessa

2018-05-01

For integrated climate change research, the Scenario Matrix Architecture provides a tractable menu of possible emissions trajectories, socio-economic futures and policy environments. However, the future of decision support may lie in searchable databases.

OSTMED.DR®, an Osteopathic Medicine Digital Library.

PubMed

Fitterling, Lori; Powers, Elaine; Vardell, Emily

2018-01-01

The OSTMED.DR® database provides access to both citation and full-text osteopathic literature, including the Journal of the American Osteopathic Association. Currently, it is a free database searchable using basic and advanced search features.

Role of small oligomers on the amyloidogenic aggregation free-energy landscape.

PubMed

He, Xianglan; Giurleo, Jason T; Talaga, David S

2010-01-08

We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.

Computational Thermodynamics Analysis of Vaporizing Fuel Droplets in the Human Upper Airways

NASA Astrophysics Data System (ADS)

Zhang, Zhe; Kleinstreuer, Clement

The detailed knowledge of air flow structures as well as particle transport and deposition in the human lung for typical inhalation flow rates is an important precursor for dosimetry-and-health-effect studies of toxic particles as well as for targeted drug delivery of therapeutic aerosols. Focusing on highly toxic JP-8 fuel aerosols, 3-D airflow and fluid-particle thermodynamics in a human upper airway model starting from mouth to Generation G3 (G0 is the trachea) are simulated using a user-enhanced and experimentally validated finite-volume code. The temperature distributions and their effects on airflow structures, fuel vapor deposition and droplet motion/evaporation are discussed. The computational results show that the thermal effect on vapor deposition is minor, but it may greatly affect droplet deposition in human airways.

77 FR 5577 - 2002 Reopened-Previously Denied Determinations; Notice of Revised Denied Determinations on...

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2012-02-03

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... reconsideration investigation revealed that the following workers groups have not met the certification criteria.../taa/taa-- search--form.cfm under the searchable listing of determinations or by calling the Office of...

77 FR 6592 - 2002 Reopened-Previously Denied Determinations; Notice of Revised Denied Determinations on...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-08

... reconsideration investigation revealed that the following workers groups have met the certification criteria under...-- search--form.cfm under the searchable listing of determinations or by calling the Office of Trade...

77 FR 9974 - 2002 Reopened-Previously Denied Determinations; Notice of Negative Determinations On...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-21

... reconsideration investigation revealed that the following workers groups have not met the certification criteria.../taa--search--form.cfm under the searchable listing of determinations or by calling the Office of Trade...

76 FR 77558 - 2002 Reopened-Previously Denied Determinations; Notice of Revised Denied Determinations on...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-13

... reconsideration investigation revealed that the following workers groups have met the certification criteria under... are available on the Department's Web site at tradeact/taa/taa--search--form.cfm under the searchable...

FACTOR FINDER CD-ROM

EPA Science Inventory

The Factor Finder CD-ROM is a user-friendly, searchable tool used to locate exposure factors and sociodemographic data for user-defined populations. Factor Finder improves the exposure assessors and risk assessors (etc.) ability to efficiently locate exposure-related informatio...

Vasculitis Syndromes of the Central and Peripheral Nervous Systems

MedlinePlus

... VCRC, www.rarediseasesnetwork.org/vcrc/ ), a network of academic medical centers, patient support organizations, and clinical research ... NIH RePORTER ( http://projectreporter.nih.gov ), a searchable database of current and past research projects supported by ...

SeaBIRD: A Flexible and Intuitive Planetary Datamining Infrastructure

NASA Astrophysics Data System (ADS)

Politi, R.; Capaccioni, F.; Giardino, M.; Fonte, S.; Capria, M. T.; Turrini, D.; De Sanctis, M. C.; Piccioni, G.

2018-04-01

Description of SeaBIRD (Searchable and Browsable Infrastructure for Repository of Data), a software and hardware infrastructure for multi-mission planetary datamining, with web-based GUI and API set for the integration in users' software.

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

Abercrombie, Robert K; Udoeyop, Akaninyene W

This work examines a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives,more » and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain we investigated.« less

Automated ocean color product validation for the Southern California Bight

NASA Astrophysics Data System (ADS)

Davis, Curtiss O.; Tufillaro, Nicholas; Jones, Burt; Arnone, Robert

2012-06-01

Automated match ups allow us to maintain and improve the products of current satellite ocean color sensors (MODIS, MERIS), and new sensors (VIIRS). As part of the VIIRS mission preparation, we have created a web based automated match up tool that provides access to searchable fields for date, site, and products, and creates match-ups between satellite (MODIS, MERIS, VIIRS), and in-situ measurements (HyperPRO and SeaPRISM). The back end of the system is a 'mySQL' database, and the front end is a `php' web portal with pull down menus for searchable fields. Based on selections, graphics are generated showing match-ups and statistics, and ascii files are created for downloads for the matchup data. Examples are shown for matching the satellite data with the data from Platform Eureka SeaPRISM off L.A. Harbor in the Southern California Bight.

Searchable attribute-based encryption scheme with attribute revocation in cloud storage.

PubMed

Wang, Shangping; Zhao, Duqiao; Zhang, Yaling

2017-01-01

Attribute based encryption (ABE) is a good way to achieve flexible and secure access control to data, and attribute revocation is the extension of the attribute-based encryption, and the keyword search is an indispensable part for cloud storage. The combination of both has an important application in the cloud storage. In this paper, we construct a searchable attribute-based encryption scheme with attribute revocation in cloud storage, the keyword search in our scheme is attribute based with access control, when the search succeeds, the cloud server returns the corresponding cipher text to user and the user can decrypt the cipher text definitely. Besides, our scheme supports multiple keywords search, which makes the scheme more practical. Under the assumption of decisional bilinear Diffie-Hellman exponent (q-BDHE) and decisional Diffie-Hellman (DDH) in the selective security model, we prove that our scheme is secure.

Data, Metadata - Who Cares?

NASA Astrophysics Data System (ADS)

Baumann, Peter

2013-04-01

There is a traditional saying that metadata are understandable, semantic-rich, and searchable. Data, on the other hand, are big, with no accessible semantics, and just downloadable. Not only has this led to an imbalance of search support form a user perspective, but also underneath to a deep technology divide often using relational databases for metadata and bespoke archive solutions for data. Our vision is that this barrier will be overcome, and data and metadata become searchable likewise, leveraging the potential of semantic technologies in combination with scalability technologies. Ultimately, in this vision ad-hoc processing and filtering will not distinguish any longer, forming a uniformly accessible data universe. In the European EarthServer initiative, we work towards this vision by federating database-style raster query languages with metadata search and geo broker technology. We present our approach taken, how it can leverage OGC standards, the benefits envisaged, and first results.

Scientometric methods for identifying emerging technologies

DOEpatents

Abercrombie, Robert K; Schlicher, Bob G; Sheldon, Frederick T

2015-11-03

Provided is a method of generating a scientometric model that tracks the emergence of an identified technology from initial discovery (via original scientific and conference literature), through critical discoveries (via original scientific, conference literature and patents), transitioning through Technology Readiness Levels (TRLs) and ultimately on to commercial application. During the period of innovation and technology transfer, the impact of scholarly works, patents and on-line web news sources are identified. As trends develop, currency of citations, collaboration indicators, and on-line news patterns are identified. The combinations of four distinct and separate searchable on-line networked sources (i.e., scholarly publications and citation, worldwide patents, news archives, and on-line mapping networks) are assembled to become one collective network (a dataset for analysis of relations). This established network becomes the basis from which to quickly analyze the temporal flow of activity (searchable events) for the example subject domain.

Polyamine analogue antidiarrheals: a structure-activity study.

PubMed

Bergeron, R J; Wiegand, J; McManis, J S; Weimar, W R; Smith, R E; Algee, S E; Fannin, T L; Slusher, M A; Snyder, P S

2001-01-18

The syntheses of a group of spermine polyamine analogues and their evaluation as antidiarrheals are described. Each compound was assessed in a rodent castor oil-induced diarrhea model for its ability to reduce stool output and weight loss in a dose-dependent manner. The spermine pharmacophore is shown to be an excellent platform from which to construct antidiarrheals. The activity of the compounds is very dependent on both the nature of the terminal alkyl groups and the geometry of the methylene spacers separating the nitrogens. The toxicity profile is also quite dependent on these same structural features. On the basis of subcutaneous dose-response data and toxicity profiles, two compounds, N(1),N(12)-diisopropylspermine and N(1),N(12)-diethylspermine, were taken forward into more complete evaluation. These measurements included formal acute and chronic toxicity trials, drug and metabolic tissue distribution studies, and assessment of the impact of these analogues on tissue polyamine pools. Finally, the remarkable activity of N,N'-bis[3-(ethylamino)propyl]-trans-1,4-cyclohexanediamine underscores the need to further explore this framework as a pharmacophore for the construction of other antidiarrheal agents.

Characteristics of silver nanoparticles in vehicles for biological applications.

PubMed

Kejlová, Kristina; Kašpárková, Věra; Krsek, Daniel; Jírová, Dagmar; Kolářová, Hana; Dvořáková, Markéta; Tománková, Kateřina; Mikulcová, Veronika

2015-12-30

Silver nanoparticles (AgNPs) have been used for decades as anti-bacterial agents in various industrial fields such as cosmetics, health industry, food storage, textile coatings and environmental applications, although their toxicity is not fully recognized yet. Antimicrobial and catalytic activity of AgNPs depends on their size as well as structure, shape, size distribution, and physico-chemical environment. The unique properties of AgNPs require novel or modified toxicological methods for evaluation of their toxic potential combined with robust analytical methods for characterization of nanoparticles applied in relevant vehicles, e.g., culture medium with/without serum and phosphate buffered saline. Copyright © 2015 Elsevier B.V. All rights reserved.

A toxicologic and dermatologic assessment of cinnamyl phenylpropyl materials when used as fragrance ingredients.

PubMed

Belsito, D; Bickers, D; Bruze, M; Calow, P; Dagli, M; Fryer, A D; Greim, H; Miyachi, Y; Saurat, J H; Sipes, I G

2011-12-01

The cinnamyl phenylpropyl fragrance ingredients are a diverse group of chemical structures that have similar metabolic and toxicity profiles. A toxicological and dermatological review of these fragrance ingredients is presented. The common characteristic structural element of cinnamyl phenylpropyl materials is an aryl substituted primary alcohol/aldehyde/ester. For high end users, calculated maximum dermal exposures vary from 0.14% to 0.72%; systemic exposures vary from 0.0002 to 0.0280 mg/kg/day. Human dermatological studies show that these materials are not generally irritants or sensitizers at lower exposures from consumer products. Reactions (0.9%) in fragrance sensitive patients were observed with 3-phenyl-1-propanol at 5% in petrolatum. The cinnamyl phenylpropyl materials had low acute toxicity and no significant toxicity in repeat dose oral or dermal toxicity studies. No mutagenic or genotoxic activity in bacteria and mammalian cell line assays was observed. The cinnamyl phenylpropyl alcohol materials participate in the same beta oxidation pathways as their parent cinnamic acid derivatives, including common routes of absorption, distribution, and metabolic detoxification, and exhibit similar toxicological endpoints. Based on the review of available data, it is concluded that these materials would not present a safety concern at current levels of use as fragrance ingredients. Copyright © 2011 Elsevier Ltd. All rights reserved.

EFFECT OF NITRATE-BASED BIOREMEDIATION ON CONTAMINANT DISTRIBUTION AND SEDIMENT TOXICITY-COLUMN STUDY

EPA Science Inventory

A laboratory column study was set up to evaluate changes in contaminant distribution and sediment toxicity following nitrate-based bioremediation and to correlate toxicity reduction with loss of fuel components. Glass columns were packed with sediment from an aquifer that had be...

In silico quantitative structure-toxicity relationship study of aromatic nitro compounds.

PubMed

Pasha, Farhan Ahmad; Neaz, Mohammad Morshed; Cho, Seung Joo; Ansari, Mohiuddin; Mishra, Sunil Kumar; Tiwari, Sharvan

2009-05-01

Small molecules often have toxicities that are a function of molecular structural features. Minor variations in structural features can make large difference in such toxicity. Consequently, in silico techniques may be used to correlate such molecular toxicities with their structural features. Relative to nine different sets of aromatic nitro compounds having known observed toxicities against different targets, we developed ligand-based 2D quantitative structure-toxicity relationship models using 20 selected topological descriptors. The topological descriptors have several advantages such as conformational independency, facile and less time-consuming computation to yield good results. Multiple linear regression analysis was used to correlate variations of toxicity with molecular properties. The information index on molecular size, lopping centric index and Kier flexibility index were identified as fundamental descriptors for different kinds of toxicity, and further showed that molecular size, branching and molecular flexibility might be particularly important factors in quantitative structure-toxicity relationship analysis. This study revealed that topological descriptor-guided quantitative structure-toxicity relationship provided a very useful, cost and time-efficient, in silico tool for describing small-molecule toxicities.

Development and Uses of Offline and Web-Searchable Metabolism Databases - The Case of Benzo[a]pyrene.

PubMed

Rendic, Slobodan P; Guengerich, Frederick P

2018-01-01

The present work describes development of offline and web-searchable metabolism databases for drugs, other chemicals, and physiological compounds using human and model species, prompted by the large amount of data published after year 1990. The intent was to provide a rapid and accurate approach to published data to be applied both in science and to assist therapy. Searches for the data were done using the Pub Med database, accessing the Medline database of references and abstracts. In addition, data presented at scientific conferences (e.g., ISSX conferences) are included covering the publishing period beginning with the year 1976. Application of the data is illustrated by the properties of benzo[a]pyrene (B[a]P) and its metabolites. Analysis show higher activity of P450 1A1 for activation of the (-)- isomer of trans-B[a]P-7,8-diol, while P4501B1 exerts higher activity for the (+)- isomer. P450 1A2 showed equally low activity in the metabolic activation of both isomers. The information collected in the databases is applicable in prediction of metabolic drug-drug and/or drug-chemical interactions in clinical and environmental studies. The data on the metabolism of searched compound (exemplified by benzo[a]pyrene and its metabolites) also indicate toxicological properties of the products of specific reactions. The offline and web-searchable databases had wide range of applications (e.g. computer assisted drug design and development, optimization of clinical therapy, toxicological applications) and adjustment in everyday life styles. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

In vitro investigation of oxide nanoparticle and carbon nanotube toxicity and intracellular accumulation in A549 human pneumocytes.

PubMed

Simon-Deckers, A; Gouget, B; Mayne-L'hermite, M; Herlin-Boime, N; Reynaud, C; Carrière, M

2008-11-20

If released in the environment, nanomaterials might be inhaled by populations and cause damage to the deepest regions of the respiratory tract, i.e., the alveolar compartment. To model this situation, we studied the response of A549 human pneumocytes after exposure to aluminium oxide or titanium oxide nanoparticles, and to multi-walled carbon nanotubes. The influence of size, crystalline structure and chemical composition was investigated. After a detailed identification of nanomaterial physico-chemical characteristics, cells were exposed in vitro and viability and intracellular accumulation were assessed. In our conditions, carbon nanotubes were more toxic than metal oxide nanoparticles. Our results confirmed that both nanotubes and nanoparticles are able to rapidly enter into cells, and distribute in the cytoplasm and intracellular vesicles. Among nanoparticles, we demonstrate significant difference in biological response as a function of size, crystalline phase and chemical composition. Their toxicity was globally lower than nanotubes toxicity. Among nanotubes, the length did not influence cytotoxicity, neither the presence of metal catalyst impurities.

[Copper nanoparticles as modulators of apoptosis and structural changes in some organs].

PubMed

Sizova, E A; Miroshnikov, S A; Poliakova, V S; Lebedev, S V; Glushchenko, N N

2013-01-01

The effect of repeated intramuscular injection into the organism of copper nanoparticles (CNP) with the diameter of 103 nm on the index of cell readiness to apoptosis and the structure of liver, spleen, kidney, as well as sensomotor cerebral cortex, was studied in 78 male Wistar rats. CNP were injected once per week for 12 weeks. The organs were studied using histological, immunohistochemical and morphometric methods. It was found that after the injections, CNP were distributed into organs and tissues of animals causing structural changes that were specific for eaach tissue. Toxicity of CNP in respect to microgliocytes was demonstrated at a dose of 2 mg/kg, hepatotoxicity and nephrotoxicity--at 6 mg/kg. The increase of CNP load on the organism up to toxic threshold (maximum tolerated dose) resulted in the appearance of signs of dystrophy and tissue necrosis. The data obtained suggest the application of an index of cell readiness to apoptosis, as assessed by caspase 3 expression, as a criterion for evaluation of CNP injection safety.

77 FR 3506 - 2002 Reopened-Previously Denied Determinations; Notice of Revised Denied Determinations On...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-24

... reconsideration investigation revealed that the following workers groups have met the certification criteria under... available on the Department's Web site at tradeact/taa/taa--search--form.cfm under the searchable listing of...

Technical Support Project for Cleaning Up Contaminated Sites - Expertise Directory

EPA Pesticide Factsheets

This directory is searchable and provides a snapshot of the various types of expertise possessed by the current members of the three Technical Support Project forums. It is based on input provided by the members themselves.

Trace element distribution in the rat cerebellum

NASA Astrophysics Data System (ADS)

Kwiatek, W. M.; Long, G. J.; Pounds, J. G.; Reuhl, K. R.; Hanson, A. L.; Jones, K. W.

1990-04-01

Spatial distributions and concentrations of trace elements (TE) in the brain are important because TE perform catalytic and structural functions in enzymes which regulate brain function and development. We have investigated the distributions of TE in rat cerebellum. Structures were sectioned and analyzed by the Synchrotron Radiation Induced X-ray Emission (SRIXE) method using the NSLS X-26 white-light microprobe facility. Advantages important for TE analysis of biological specimens with X-ray microscopy include short time of measurement, high brightness and flux, good spatial resolution, multielemental detection, good sensitivity, and nondestructive irradiation. Trace elements were measured in thin rat brain sections of 20 μm thickness. The analyses were performed on sample volumes as small as 0.2 nl with Minimum Detectable Limits (MDL) of 50 ppb wet weight for Fe, 100 ppb wet weight for Cu, and Zn, and 1 ppm wet weight for Pb. The distribution of TE in the molecular cell layer, granule cell layer and fiber tract of rat cerebella was investigated. Both point analyses and two-dimensional semiquantitative mapping of the TE distribution in a section were used. All analyzed elements were observed in each structure of the cerebellum except mercury which was not observed in granule cell layer or fiber tract. This approach permits an exacting correlation of the TE distribution in complex structure with the diet, toxic elements, and functional status of the animal.

Embryonic exposure to model naphthenic acids delays growth and hatching in the pond snail Lymnaea stagnalis.

PubMed

Johnston, Christina U; Clothier, Lindsay N; Quesnel, Dean M; Gieg, Lisa M; Chua, Gordon; Hermann, Petra M; Wildering, Willem C

2017-02-01

Naphthenic acids (NAs), a class of structurally diverse carboxylic acids with often complex ring structures and large aliphatic tail groups, are important by-products of many petrochemical processes including the oil sands mining activity of Northern Alberta. While it is evident that NAs have both acute and chronic harmful effects on many organisms, many aspects of their toxicity remain to be clarified. Particularly, while substantive data sets have been collected on NA toxicity in aquatic prokaryote and vertebrate model systems, to date, nothing is known about the toxic effects of these compounds on the embryonic development of aquatic invertebrate taxa, including freshwater mollusks. This study examines under laboratory conditions the toxicity of NAs extracted from oil sands process water (OSPW) and the low-molecular weight model NAs cyclohexylsuccinic acid (CHSA), cyclohexanebutyric acid (CHBA), and 4-tert-butylcyclohexane carboxylic acid (4-TBCA) on embryonic development of the snail Lymnaea stagnalis, a common freshwater gastropod with a broad Palearctic distribution. Evidence is provided for concentration-dependent teratogenic effects of both OSPW-derived and model NAs with remarkably similar nominal threshold concentrations between 15 and 20 mg/L and 28d EC 50 of 31 mg/L. In addition, the data provide evidence for substantial toxicokinetic differences between CHSA, CHBA and 4-TBCA. Together, our study introduces Lymnaea stagnalis embryonic development as an effective model to assay NA-toxicity and identifies molecular architecture as a potentially important toxicokinetic parameter in the toxicity of low-molecular weight NA in embryonic development of aquatic gastropods. Copyright © 2016 Elsevier Ltd. All rights reserved.

Cross-Diffusion Induced Turing Instability and Amplitude Equation for a Toxic-Phytoplankton-Zooplankton Model with Nonmonotonic Functional Response

NASA Astrophysics Data System (ADS)

Han, Renji; Dai, Binxiang

2017-06-01

The spatiotemporal pattern induced by cross-diffusion of a toxic-phytoplankton-zooplankton model with nonmonotonic functional response is investigated in this paper. The linear stability analysis shows that cross-diffusion is the key mechanism for the formation of spatial patterns. By taking cross-diffusion rate as bifurcation parameter, we derive amplitude equations near the Turing bifurcation point for the excited modes in the framework of a weakly nonlinear theory, and the stability analysis of the amplitude equations interprets the structural transitions and stability of various forms of Turing patterns. Furthermore, we illustrate the theoretical results via numerical simulations. It is shown that the spatiotemporal distribution of the plankton is homogeneous in the absence of cross-diffusion. However, when the cross-diffusivity is greater than the critical value, the spatiotemporal distribution of all the plankton species becomes inhomogeneous in spaces and results in different kinds of patterns: spot, stripe, and the mixture of spot and stripe patterns depending on the cross-diffusivity. Simultaneously, the impact of toxin-producing rate of toxic-phytoplankton (TPP) species and natural death rate of zooplankton species on pattern selection is also explored.

MISSE in the Materials and Processes Technical Information System (MAPTIS )

NASA Technical Reports Server (NTRS)

Burns, DeWitt; Finckenor, Miria; Henrie, Ben

2013-01-01

Materials International Space Station Experiment (MISSE) data is now being collected and distributed through the Materials and Processes Technical Information System (MAPTIS) at Marshall Space Flight Center in Huntsville, Alabama. MISSE data has been instrumental in many programs and continues to be an important source of data for the space community. To facilitate great access to the MISSE data the International Space Station (ISS) program office and MAPTIS are working to gather this data into a central location. The MISSE database contains information about materials, samples, and flights along with pictures, pdfs, excel files, word documents, and other files types. Major capabilities of the system are: access control, browsing, searching, reports, and record comparison. The search capabilities will search within any searchable files so even if the desired meta-data has not been associated data can still be retrieved. Other functionality will continue to be added to the MISSE database as the Athena Platform is expanded

Community Structure of Macrobiota and Environmental Parameters in Shallow Water Hydrothermal Vents off Kueishan Island, Taiwan

PubMed Central

Chan, Benny Kwok Kan; Wang, Teng-Wei; Chen, Pin-Chen; Lin, Chia-Wei; Chan, Tin-Yam; Tsang, Ling Ming

2016-01-01

Hydrothermal vents represent a unique habitat in the marine ecosystem characterized with high water temperature and toxic acidic chemistry. Vents are distributed at depths ranging from a few meters to several thousand meters. The biological communities of shallow-water vents have, however, been insufficiently studied in most biogeographic areas. We attempted to characterize the macrofauna and macroflora community inhabiting the shallow-water vents off Kueishan Island, Taiwan, to identify the main abiotic factors shaping the community structure and the species distribution. We determined that positively buoyant vent fluid exhibits a more pronounced negative impact to species on the surface water than on the bottom layer. Species richness increased with horizontal distance from the vent, and continuing for a distance of 2000 m, indicating that the vent fluid may exert a negative impact over several kilometers. The community structure off Kueishan Island displayed numerous transitions along the horizontal gradient, which were broadly congruent with changes in environmental conditions. Combination of variation in Ca2+, Cl-, temperature, pH and depth were revealed to show the strongest correlation with the change in benthic community structure, suggesting multiple factors of vent fluid were influencing the associated fauna. Only the vent crabs of Kueishan Island may have an obligated relationship with vents and inhabit the vent mouths because other fauna found nearby are opportunistic taxa that are more tolerant to acidic and toxic environments. PMID:26849440

Interindividual registration and dose mapping for voxelwise population analysis of rectal toxicity in prostate cancer radiotherapy

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

Dréan, Gaël; Acosta, Oscar, E-mail: Oscar.Acosta@univ-rennes1.fr; Simon, Antoine

2016-06-15

Purpose: Recent studies revealed a trend toward voxelwise population analysis in order to understand the local dose/toxicity relationships in prostate cancer radiotherapy. Such approaches require, however, an accurate interindividual mapping of the anatomies and 3D dose distributions toward a common coordinate system. This step is challenging due to the high interindividual variability. In this paper, the authors propose a method designed for interindividual nonrigid registration of the rectum and dose mapping for population analysis. Methods: The method is based on the computation of a normalized structural description of the rectum using a Laplacian-based model. This description takes advantage of themore » tubular structure of the rectum and its centerline to be embedded in a nonrigid registration-based scheme. The performances of the method were evaluated on 30 individuals treated for prostate cancer in a leave-one-out cross validation. Results: Performance was measured using classical metrics (Dice score and Hausdorff distance), along with new metrics devised to better assess dose mapping in relation with structural deformation (dose-organ overlap). Considering these scores, the proposed method outperforms intensity-based and distance maps-based registration methods. Conclusions: The proposed method allows for accurately mapping interindividual 3D dose distributions toward a single anatomical template, opening the way for further voxelwise statistical analysis.« less

Spatial dynamics of a nutrient-phytoplankton system with toxic effect on phytoplankton.

PubMed

Chakraborty, Subhendu; Tiwari, P K; Misra, A K; Chattopadhyay, J

2015-06-01

The production of toxins by some species of phytoplankton is known to have several economic, ecological, and human health impacts. However, the role of toxins on the spatial distribution of phytoplankton is not well understood. In the present study, the spatial dynamics of a nutrient-phytoplankton system with toxic effect on phytoplankton is investigated. We analyze the linear stability of the system and obtain the condition for Turing instability. In the presence of toxic effect, we find that the distribution of nutrient and phytoplankton becomes inhomogeneous in space and results in different patterns, like stripes, spots, and the mixture of them depending on the toxicity level. We also observe that the distribution of nutrient and phytoplankton shows spatiotemporal oscillation for certain toxicity level. Copyright © 2015 Elsevier Inc. All rights reserved.

Acute oral toxicity and biodistribution study of zinc-aluminium-levodopa nanocomposite

NASA Astrophysics Data System (ADS)

Kura, Aminu Umar; Saifullah, Bullo; Cheah, Pike-See; Hussein, Mohd Zobir; Azmi, Norazrina; Fakurazi, Sharida

2015-03-01

Layered double hydroxide (LDH) is an inorganic-organic nano-layered material that harbours drug between its two-layered sheets, forming a sandwich-like structure. It is attracting a great deal of attention as an alternative drug delivery (nanodelivery) system in the field of pharmacology due to their relative low toxic potential. The production of these nanodelivery systems, aimed at improving human health through decrease toxicity, targeted delivery of the active compound to areas of interest with sustained release ability. In this study, we administered zinc-aluminium-LDH-levodopa nanocomposite (ZAL) and zinc-aluminium nanocomposite (ZA) to Sprague Dawley rats to evaluate for acute oral toxicity following OECD guidelines. The oral administration of ZAL and ZA at a limit dose of 2,000 mg/kg produced neither mortality nor acute toxic signs throughout 14 days of the observation. The percentage of body weight gain of the animals showed no significant difference between control and treatment groups. Animal from the two treated groups gained weight continuously over the study period, which was shown to be significantly higher than the weight at the beginning of the study ( P < 0.05). Biochemical analysis of animal serum showed no significant difference between rats treated with ZAL, ZA and controls. There was no gross lesion or histopathological changes observed in vital organs of the rats. The results suggested that ZAL and ZA at 2,000 mg/kg body weight in rats do not induce acute toxicity in the animals. Elemental analysis of tissues of treated animals demonstrated the wider distribution of the nanocomposite including the brain. In summary, findings of acute toxicity tests in this study suggest that zinc-aluminium nanocomposite intercalated with and the un-intercalated were safe when administered orally in animal models for short periods of time. It also highlighted the potential distribution ability of Tween-80 coated nanocomposite after oral administration.

7 CFR 226.14 - Claims against institutions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Agriculture Regulations of the Department of Agriculture (Continued) FOOD AND NUTRITION SERVICE, DEPARTMENT OF AGRICULTURE CHILD NUTRITION PROGRAMS CHILD AND ADULT CARE FOOD PROGRAM Payment Provisions § 226.14 Claims... searchable records of funds recovery activities. If the State agency determines that a sponsoring...

Dr. George Koob: "Alcohol Use Disorders Are a Major Problem..."

MedlinePlus

... 662-HELP (4357) or the Substance Abuse Treatment Facility Locator, an online, searchable directory of alcohol and drug abuse programs located around the country. Read More "Rethinking Drinking" Articles Rethinking Drinking / The Importance of Drinking Patterns / Dr. George Koob: "Alcohol use ...

EPA'S REPORT ON THE ENVIRONMENT (2003 Draft)

EPA Science Inventory

The RoE presents information on environmental indicators in the areas of air, water, land, human health, and ecological condition. The report is available for download and the RoE information is searchable via an on-line database site: www.epa.gov/roe.

Switch on Micro*scope!

ERIC Educational Resources Information Center

Roland, Sarah; Bahr, Michele; Olendzenski, Lorraine; Patterson, David J.

2005-01-01

Scientists at the Marine Biological Laboratory in Woods Hole, Massachusetts, have created micro*scope, a free, searchable knowledge environment for exploring the microbial world. Microbiology can easily be incorporated into the curriculum, because microbial communities are easy to access. Organisms grow quickly, making certain arrays of…

AN EPA SPONSORED LITERATURE REVIEW DATABASE TO SUPPORT STRESSOR IDENTIFICATION

EPA Science Inventory

The Causal Analysis/Diagnosis Decision Information System (CADDIS) is an EPA decision-support system currently under development for evaluating the biological impact of stressors on water bodies. In support of CADDIS, EPA is developing CADLIT, a searchable database of the scient...

The International Outer Planets Watch atmospheres node database of giant-planet images

NASA Astrophysics Data System (ADS)

Hueso, R.; Legarreta, J.; Sánchez-Lavega, A.; Rojas, J. F.; Gómez-Forrellad, J. M.

2011-10-01

The Atmospheres Node of the International Outer Planets Watch (IOPW) is aimed to encourage the observations and study of the atmospheres of the Giant Planets. One of its main activities is to provide an interaction between the professional and amateur astronomical communities maintaining an online and fully searchable database of images of the giant planets obtained from amateur astronomers and available to both professional and amateurs [1]. The IOPW database contains about 13,000 image observations of Jupiter and Saturn obtained in the visible range with a few contributions of Uranus and Neptune. We describe the organization and structure of the database as posted in the Internet and in particular the PVOL software (Planetary Virtual Observatory & Laboratory) designed to manage the site and based in concepts from Virtual Observatory projects.

MoonProt: a database for proteins that are known to moonlight

PubMed Central

Mani, Mathew; Chen, Chang; Amblee, Vaishak; Liu, Haipeng; Mathur, Tanu; Zwicke, Grant; Zabad, Shadi; Patel, Bansi; Thakkar, Jagravi; Jeffery, Constance J.

2015-01-01

Moonlighting proteins comprise a class of multifunctional proteins in which a single polypeptide chain performs multiple biochemical functions that are not due to gene fusions, multiple RNA splice variants or pleiotropic effects. The known moonlighting proteins perform a variety of diverse functions in many different cell types and species, and information about their structures and functions is scattered in many publications. We have constructed the manually curated, searchable, internet-based MoonProt Database (http://www.moonlightingproteins.org) with information about the over 200 proteins that have been experimentally verified to be moonlighting proteins. The availability of this organized information provides a more complete picture of what is currently known about moonlighting proteins. The database will also aid researchers in other fields, including determining the functions of genes identified in genome sequencing projects, interpreting data from proteomics projects and annotating protein sequence and structural databases. In addition, information about the structures and functions of moonlighting proteins can be helpful in understanding how novel protein functional sites evolved on an ancient protein scaffold, which can also help in the design of proteins with novel functions. PMID:25324305

General baseline toxicity QSAR for nonpolar, polar and ionisable chemicals and their mixtures in the bioluminescence inhibition assay with Aliivibrio fischeri.

PubMed

Escher, Beate I; Baumer, Andreas; Bittermann, Kai; Henneberger, Luise; König, Maria; Kühnert, Christin; Klüver, Nils

2017-03-22

The Microtox assay, a bioluminescence inhibition assay with the marine bacterium Aliivibrio fischeri, is one of the most popular bioassays for assessing the cytotoxicity of organic chemicals, mixtures and environmental samples. Most environmental chemicals act as baseline toxicants in this short-term screening assay, which is typically run with only 30 min of exposure duration. Numerous Quantitative Structure-Activity Relationships (QSARs) exist for the Microtox assay for nonpolar and polar narcosis. However, typical water pollutants, which have highly diverse structures covering a wide range of hydrophobicity and speciation from neutral to anionic and cationic, are often outside the applicability domain of these QSARs. To include all types of environmentally relevant organic pollutants we developed a general baseline toxicity QSAR using liposome-water distribution ratios as descriptors. Previous limitations in availability of experimental liposome-water partition constants were overcome by reliable prediction models based on polyparameter linear free energy relationships for neutral chemicals and the COSMOmic model for charged chemicals. With this QSAR and targeted mixture experiments we could demonstrate that ionisable chemicals fall in the applicability domain. Most investigated water pollutants acted as baseline toxicants in this bioassay, with the few outliers identified as uncouplers or reactive toxicants. The main limitation of the Microtox assay is that chemicals with a high melting point and/or high hydrophobicity were outside of the applicability domain because of their low water solubility. We quantitatively derived a solubility cut-off but also demonstrated with mixture experiments that chemicals inactive on their own can contribute to mixture toxicity, which is highly relevant for complex environmental mixtures, where these chemicals may be present at concentrations below the solubility cut-off.

Role of salicylic acid in resistance to cadmium stress in plants.

PubMed

Liu, Zhouping; Ding, Yanfei; Wang, Feijuan; Ye, Yaoyao; Zhu, Cheng

2016-04-01

We review and introduce the importance of salicylic acid in plants under cadmium stress, and provide insights into potential regulatory mechanisms for alleviating cadmium toxicity. Cadmium (Cd) is a widespread and potentially toxic environmental pollutant, originating mainly from rapid industrial processes, the application of fertilizers, manures and sewage sludge, and urban activities. It is easily taken up by plants, resulting in obvious toxicity symptoms, including growth retardation, leaf chlorosis, leaf and root necrosis, altered structures and ultrastructures, inhibition of photosynthesis, and cell death. Therefore, alleviating Cd toxicity in plants is a major aim of plant research. Salicylic acid (SA) is a ubiquitous plant phenolic compound that has been used in many plant species to alleviate Cd toxicity by regulating plant growth, reducing Cd uptake and distribution in plants, protecting membrane integrity and stability, scavenging reactive oxygen species and enhancing antioxidant defense system, improving photosynthetic capacity. Furthermore, SA functions as a signaling molecule involved in the expression of several important genes. Significant amounts of research have focused on understanding SA functions and signaling in plants under Cd stress, but several questions still remain unanswered. In this article, the influence of SA on Cd-induced stress in plants and the potential regulation mechanism for alleviating Cd toxicity are reviewed.

Distribution of Drug Molecules in Lipid Membranes: Neutron Diffraction and MD Simulations.

NASA Astrophysics Data System (ADS)

Boggara, Mohan; Mihailescu, Ella; Krishnamoorti, Ramanan

2009-03-01

Non-steroidal anti-inflammatory drugs (NSAIDs) e.g. Aspirin and Ibuprofen, with chronic usage cause gastro intestinal (GI) toxicity. It has been shown experimentally that NSAIDs pre-associated with phospholipids reduce the GI toxicity and also increase the therapeutic activity of these drugs compared to the unmodified ones. In this study, using neutron diffraction, the DOPC lipid bilayer structure (with and without drug) as well as the distribution of a model NSAID (Ibuprofen) as a function of its position along the membrane normal was obtained at sub-nanometer resolution. It was found that the bilayer thickness reduces as the drug is added. Further, the results are successfully compared with atomistic Molecular Dynamics simulations. Based on this successful comparison and motivated by atomic details from MD, quasi-molecular modeling of the lipid membrane is being carried out and will be presented. The above study is expected to provide an effective methodology to design drug delivery nanoparticles based on a variety of soft condensed matter such as lipids or polymers.

Absorption, Distribution, Metabolism and Excretion of 3-MCPD 1-Monopalmitate after Oral Administration in Rats.

PubMed

Gao, Boyan; Liu, Man; Huang, Guoren; Zhang, Zhongfei; Zhao, Yue; Wang, Thomas T Y; Zhang, Yaqiong; Liu, Jie; Yu, Liangli

2017-03-29

Fatty acid esters of monochloropropane 1,2-diol (3-MCPD) are processing-induced toxicants and have been detected in several food categories. This study investigated the absorption, distribution, metabolism, and excretion of 3-MCPD esters in Sprague-Dawley (SD) rats using 3-MCPD 1-monopalmitate as the probe compound. The kinetics of 3-MCPD 1-monopalmitate in plasma was investigated using SD rats, and the results indicated that 3-MCPD 1-monopalmitate was absorbed directly in vivo and metabolized. Its primary metabolites in the liver, kidney, testis, brain, plasma, and urine were tentatively identified and measured at 6, 12, 24, and 48 h after oral administration. Structures were proposed for eight metabolites. 3-MCPD 1-monopalmitate was converted to free 3-MCPD, which formed the phase II metabolites. All of the metabolites were chlorine-related chemical components; most of them existed in urine, reflecting the excretion pattern of 3-MCPD esters. Understanding the metabolism of 3-MCPD esters in vivo is critical for assessing their toxicities.

Computerization of ALDOT R & D library titles : a project for the Alabama Department of Transportation

DOT National Transportation Integrated Search

2003-06-01

The Alabama Department of Transportation (ALDOT) Research and Development (R&D) Bureau wished to catalog the paper publications in its library and produce a searchable database that allows an internet user easily to identify if a particular document ...

78 FR 19243 - Privacy Act of 1974; System of Records

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-29

... applicant; or stored in searchable database and retrievable by patent number. Safeguards: Buildings employ... DEPARTMENT OF COMMERCE United States Patent and Trademark Office Privacy Act of 1974; System of Records AGENCY: United States Patent and Trademark Office, Commerce. ACTION: Notice of amendment of...

Which Online Resources Are Right for Your Collection?

ERIC Educational Resources Information Center

Pearlmutter, Jane

1999-01-01

Discusses important considerations for library media specialists creating a virtual-resources-collection policy, including selecting the right resources, navigating licensing fees, and free, searchable online sources. A sidebar lists resources for evaluating Web sites and places that lead to recommended sites for students. (AEF)

Protecting the Privacy of Individuals in Terrorist Tracking Applications

DTIC Science & Technology

2005-04-01

THE PRIVACY OF INDIVIDUALS IN TERRORIST TRACKING APPLICATIONS 6. AUTHOR(S) Teresa Lunt, Paul Aoki, Dirk Balfanz , Glenn Durfee, Philippe Golle...in Data Mining and Knowledge Discovery. 3) Brent Waters, Dirk Balfanz , Glenn Durfee, and Diana Smetters. Building an encrypted and searchable audit

EDUCATIONPLANNER.CA: An External Review

ERIC Educational Resources Information Center

Atkinson, Al

2009-01-01

The Education Planner website provides a searchable database of approximately 1,700 undergraduate post-secondary programs in British Columbia (BC). It is intended as a "one-start entry point" for students looking for post-secondary options. This independent review of Education Planner was undertaken to determine its overall…

WWW.LCACCESS -- GLOBAL DIRECTORY OF LCI RESOURCES

EPA Science Inventory

LCAccess is a USEPA sponsored web-site intended to promote the use of Life Cycle Assessments in business decision-making by facilitating access to data sources useful in developing a life cycle inventory (LCI). While LCAccess will not itself contain data, it will be a searchable...

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

Tobler, Matt; Watson, Gordon; Leavitt, Dennis

Radiotherapy plays a key role in the definitive or adjuvant management of patients with mesothelioma of the pleural surface. Many patients are referred for radiation with intact lung following biopsy or subtotal pleurectomy. Delivery of efficacious doses of radiation to the pleural lining while avoiding lung parenchyma toxicity has been a difficult technical challenge. Using opposed photon fields produce doses in lung that result in moderate-to-severe pulmonary toxicity in 100% of patients treated. Combined photon-electron beam treatment, at total doses of 4250 cGy to the pleural surface, results in two-thirds of the lung volume receiving over 2100 cGy. We havemore » developed a technique using intensity-modulated photon arc therapy (IMRT) that significantly improves the dose distribution to the pleural surface with concomitant decrease in dose to lung parenchyma compared to traditional techniques. IMRT treatment of the pleural lining consists of segments of photon arcs that can be intensity modulated with varying beam weights and multileaf positions to produce a more uniform distribution to the pleural surface, while at the same time reducing the overall dose to the lung itself. Computed tomography (CT) simulation is critical for precise identification of target volumes as well as critical normal structures (lung and heart). Rotational arc trajectories and individual leaf positions and weightings are then defined for each CT plane within the patient. This paper will describe the proposed rotational IMRT technique and, using simulated isodose distributions, show the improved potential for sparing of dose to the critical structures of the lung, heart, and spinal cord.« less

The new on-line Czech Food Composition Database.

PubMed

Machackova, Marie; Holasova, Marie; Maskova, Eva

2013-10-01

The new on-line Czech Food Composition Database (FCDB) was launched on http://www.czfcdb.cz in December 2010 as a main freely available channel for dissemination of Czech food composition data. The application is based on a complied FCDB documented according to the EuroFIR standardised procedure for full value documentation and indexing of foods by the LanguaL™ Thesaurus. A content management system was implemented for administration of the website and performing data export (comma-separated values or EuroFIR XML transport package formats) by a compiler. Reference/s are provided for each published value with linking to available freely accessible on-line sources of data (e.g. full texts, EuroFIR Document Repository, on-line national FCDBs). LanguaL™ codes are displayed within each food record as searchable keywords of the database. A photo (or a photo gallery) is used as a visual descriptor of a food item. The application is searchable on foods, components, food groups, alphabet and a multi-field advanced search. Copyright © 2013 Elsevier Ltd. All rights reserved.

Data Mining the Ogle-II I-band Database for Eclipsing Binary Stars

NASA Astrophysics Data System (ADS)

Ciocca, M.

2013-08-01

The OGLE I-band database is a searchable database of quality photometric data available to the public. During Phase 2 of the experiment, known as "OGLE-II", I-band observations were made over a period of approximately 1,000 days, resulting in over 1010 measurements of more than 40 million stars. This was accomplished by using a filter with a passband near the standard Cousins Ic. The database of these observations is fully searchable using the mysql database engine, and provides the magnitude measurements and their uncertainties. In this work, a program of data mining the OGLE I-band database was performed, resulting in the discovery of 42 previously unreported eclipsing binaries. Using the software package Peranso (Vanmuster 2011) to analyze the light curves obtained from OGLE-II, the eclipsing types, the epochs and the periods of these eclipsing variables were determined, to one part in 106. A preliminary attempt to model the physical parameters of these binaries was also performed, using the Binary Maker 3 software (Bradstreet and Steelman 2004).

Review on toxicity testing with marine macroalgae and the need for method standardization--exemplified with copper and phenol.

PubMed

Eklund, Britta T; Kautsky, Lena

2003-02-01

Toxic effects on macroalgae have been compiled. Eighty-two articles have been found in literature during 1959-2000. A total of 120 substances were investigated using 65 different macroalgae species. About one-third of the tested compounds were organic substances (33%), another third metal-organic substances (35%), and the last third were oils (14%), metals (8%), detergents (7.5%) and other inorganic chemicals (2.5%). Half of the substances were only tested once on a single species. Likewise, toxicity data has only been reported for one chemical tested on a single occasion for about half of the 65 species. Thus little is known about the toxic effects on marine macroalgae. The objectives of the previous studies undertaken varied and therefore the toxicity data was presented in numerous ways, e.g. using different exposure times, temperature, light intensity, light regime, salinity, and nutrients, which makes a direct comparison of the data difficult. This review also shows that many stages in the lifecycle of macroalgae are often more sensitive to toxic substances than other aquatic organisms. Consequently, tests using macroalgae may discover toxicity earlier, which would in turn also protect the fauna. If toxic compounds have a negative affect on the distribution and growth of structurally and functionally dominating macroalgae, there may indirectly be a large and harmful influence on the whole marine coastal ecosystem. For this reason tests on macroalgae should be included in control programs along the coasts.

Classification of Chemicals Based On Structured Toxicity Information

EPA Science Inventory

Thirty years and millions of dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data within the Toxicity Reference Database (ToxRefDB). Toxicity-bas...

Variation effect on the insecticide activity of DDT analogues. A chemometric approach

NASA Astrophysics Data System (ADS)

Itoh, S.; Nagashima, U.

2002-08-01

We investigated a variation effect on the insecticide activity of DDT analogues by using the first principles electronic structure calculations and the neural network analysis. It has been found that the charge distribution at the specific atomic sites in the DDT molecule is related to their toxicity. This approach can contribute to designing a new insecticide and a new harmlessness process of the DDT analogues.

The Mauve Stinger Pelagia noctiluca (Forsskål, 1775). Distribution, Ecology, Toxicity and Epidemiology of Stings. A Review

PubMed Central

Mariottini, Gian Luigi; Giacco, Elisabetta; Pane, Luigi

2008-01-01

The toxicity of Cnidaria is a subject of concern due to its influence on humans. In particular, jellyfish blooms can highly affect human economical activities, such as bathing, fishery, tourism, etc., as well as the public health. Stinging structures of Cnidaria (nematocysts) produce remarkable effects on human skin, such as erythema, swelling, burning and vesicles, and at times further severe dermonecrotic, cardio- and neurotoxic effects, which are particularly dangerous in sensitive subjects. In several zones the toxicity of jellyfish is a very important health problem, thus it has stimulated the research on these organisms; to date toxicological research on Cnidarian venoms in the Mediterranean region is not well developed due to the weak poisonousness of venoms of jellyfish and anemones living in this area. In spite of this, during last decades several problems were also caused in the Mediterranean by stinging consequent to Cnidarian blooms mainly caused by Pelagia noctiluca (Forsskål, 1775) which is known to be the most venomous Mediterranean jellyfish. This paper reviews the knowledge on this jellyfish species, particularly considering its occurrence and toxicity. PMID:19005582

77 FR 72788 - Copyright Office Fees

Federal Register 2010, 2011, 2012, 2013, 2014

2012-12-06

... Adobe Portable Document File (PDF) format that contains searchable, accessible text (not an image... processing such statements and associated royalty payments was funded solely by the royalty fees collected... Title 17 that permits the Office to apportion up to 50 percent of the cost of processing the SOAs and...

ENVIRONMENTAL EFFECTS OF DREDGING AND DISPOSAL (E2-D2)

EPA Science Inventory

US Army Corps of Engineers public web site for the "Environmental Effects of Dredging and Disposal" ("E2-D2") searchable database of published reports and studies about environmental impacts associated with dredging and disposal operations. Many of the reports and studies are ava...

A searchable database for the genome of Phomopsis longicolla (isolate MSPL 10-6)

USDA-ARS?s Scientific Manuscript database

Phomopsis longicolla (syn. Diaporthe longicolla) is an important seed-borne fungal pathogen that primarily causes Phomopsis seed decay (PSD) in most soybean production areas worldwide. This disease severely decreases soybean seed quality by reducing seed viability and oil quality, altering seed com...

TRAC Searchable Research Library

DTIC Science & Technology

2016-05-01

network accessible document repository for technical documents and similar document artifacts. We used a model-based approach using the Vector...demonstration and model refinement. 14. SUBJECT TERMS Knowledge Management, Document Repository , Digital Library, Vector Directional Data Model...27 Figure D1. Administrator Repository Upload Page. ................................................................... D-2 Figure D2

48 CFR 5.601 - Governmentwide database of contracts.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 48 Federal Acquisition Regulations System 1 2014-10-01 2014-10-01 false Governmentwide database of... database of contracts. (a) A Governmentwide database of contracts and other procurement instruments.../contractdirectory/.This searchable database is a tool that may be used to identify existing contracts and other...

48 CFR 5.601 - Governmentwide database of contracts.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 48 Federal Acquisition Regulations System 1 2011-10-01 2011-10-01 false Governmentwide database of... database of contracts. (a) A Governmentwide database of contracts and other procurement instruments.../contractdirectory/. This searchable database is a tool that may be used to identify existing contracts and other...

48 CFR 5.601 - Governmentwide database of contracts.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 48 Federal Acquisition Regulations System 1 2012-10-01 2012-10-01 false Governmentwide database of... database of contracts. (a) A Governmentwide database of contracts and other procurement instruments.../contractdirectory/ .This searchable database is a tool that may be used to identify existing contracts and other...

48 CFR 5.601 - Governmentwide database of contracts.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 48 Federal Acquisition Regulations System 1 2013-10-01 2013-10-01 false Governmentwide database of... database of contracts. (a) A Governmentwide database of contracts and other procurement instruments.../contractdirectory/.This searchable database is a tool that may be used to identify existing contracts and other...

WWW.LCACCESS - GLOBAL DIRECTORY OF LCI RESOURCES

EPA Science Inventory

LCAccess is a USEPA sponsored web-site intended to promote the use of Life Cycle Assessment in business decision-making by facilitating access to data sources useful in developing a life cycle inventory (OCI). While LCAccess will not itself contain data, it will be a searchable g...

Semantic Networks and Social Networks

ERIC Educational Resources Information Center

Downes, Stephen

2005-01-01

Purpose: To illustrate the need for social network metadata within semantic metadata. Design/methodology/approach: Surveys properties of social networks and the semantic web, suggests that social network analysis applies to semantic content, argues that semantic content is more searchable if social network metadata is merged with semantic web…

Toward antituberculosis drugs: in silico screening of synthetic compounds against Mycobacterium tuberculosisl,d-transpeptidase 2.

PubMed

Billones, Junie B; Carrillo, Maria Constancia O; Organo, Voltaire G; Macalino, Stephani Joy Y; Sy, Jamie Bernadette A; Emnacen, Inno A; Clavio, Nina Abigail B; Concepcion, Gisela P

2016-01-01

Mycobacterium tuberculosis (Mtb) the main causative agent of tuberculosis, is the main reason why this disease continues to be a global public health threat. It is therefore imperative to find a novel antitubercular drug target that is unique to the structural machinery or is essential to the growth and survival of the bacterium. One such target is the enzyme l,d-transpeptidase 2, also known as LdtMt2, a protein primarily responsible for the catalysis of 3→3 cross-linkages that make up the mycolyl-arabinogalactan-peptidoglycan complex of Mtb. In this study, structure-based pharmacophore screening, molecular docking, and in silico toxicity evaluations were employed in screening compounds from a database of synthetic compounds. Out of the 4.5 million database compounds, 18 structures were identified as high-scoring, high-binding hits with very satisfactory absorption, distribution, metabolism, excretion, and toxicity properties. Two out of the 18 compounds were further subjected to in vitro bioactivity assays, with one exhibiting a good inhibitory activity against the Mtb H37Ra strain.

Multimedia content analysis and indexing: evaluation of a distributed and scalable architecture

NASA Astrophysics Data System (ADS)

Mandviwala, Hasnain; Blackwell, Scott; Weikart, Chris; Van Thong, Jean-Manuel

2003-11-01

Multimedia search engines facilitate the retrieval of documents from large media content archives now available via intranets and the Internet. Over the past several years, many research projects have focused on algorithms for analyzing and indexing media content efficiently. However, special system architectures are required to process large amounts of content from real-time feeds or existing archives. Possible solutions include dedicated distributed architectures for analyzing content rapidly and for making it searchable. The system architecture we propose implements such an approach: a highly distributed and reconfigurable batch media content analyzer that can process media streams and static media repositories. Our distributed media analysis application handles media acquisition, content processing, and document indexing. This collection of modules is orchestrated by a task flow management component, exploiting data and pipeline parallelism in the application. A scheduler manages load balancing and prioritizes the different tasks. Workers implement application-specific modules that can be deployed on an arbitrary number of nodes running different operating systems. Each application module is exposed as a web service, implemented with industry-standard interoperable middleware components such as Microsoft ASP.NET and Sun J2EE. Our system architecture is the next generation system for the multimedia indexing application demonstrated by www.speechbot.com. It can process large volumes of audio recordings with minimal support and maintenance, while running on low-cost commodity hardware. The system has been evaluated on a server farm running concurrent content analysis processes.

One-pot green synthesis of carbon quantum dot for biological application

NASA Astrophysics Data System (ADS)

Asghar, Khushnuma; Qasim, Mohd; Das, D.

2017-05-01

A one-pot microwave assisted method for synthesizing carbon quantum dots (CQDs) from honey is presented in this paper. The structural, morphological and optical properties of synthesized CQDs were characterized by XRD, TEM, UV-Vis spectrophotometer, and Raman techniques. The average particle size of CQDs is found to be 2 to 7 nm. The main advantage of this work is the use of inexpensive, less toxic and environmental friendly precursors and synthesis procedure for CQDs. In addition to this, the particle size of prepared CQDs was found to be ultrafine with narrow size distribution. The as-prepared CQDs, with smaller particle size, good stability, good optical properties, water dispersibility and low toxicity, show promising potential for applications in biomedical field.

Implementing the HDF-EOS5 software library for data products in the UNAVCO InSAR archive

NASA Astrophysics Data System (ADS)

Baker, Scott; Meertens, Charles; Crosby, Christopher

2017-04-01

UNAVCO is a non-profit university-governed consortium that operates the U.S. National Science Foundation (NSF) Geodesy Advancing Geosciences and EarthScope (GAGE) facility and provides operational support to the Western North America InSAR Consortium (WInSAR). The seamless synthetic aperture radar archive (SSARA) is a seamless distributed access system for SAR data and higher-level data products. Under the NASA-funded SSARA project, a user-contributed InSAR archive for interferograms, time series, and other derived data products was developed at UNAVCO. The InSAR archive development has led to the adoption of the HDF-EOS5 data model, file format, and library. The HDF-EOS software library was designed to support NASA Earth Observation System (EOS) science data products and provides data structures for radar geometry (Swath) and geocoded (Grid) data based on the HDF5 data model and file format provided by the HDF Group. HDF-EOS5 inherits the benefits of HDF5 (open-source software support, internal compression, portability, support for structural data, self-describing file metadata enhanced performance, and xml support) and provides a way to standardize InSAR data products. Instrument- and datatype-independent services, such as subsetting, can be applied to files across a wide variety of data products through the same library interface. The library allows integration with GIS software packages such as ArcGIS and GDAL, conversion to other data formats like NetCDF and GeoTIFF, and is extensible with new data structures to support future requirements. UNAVCO maintains a GitHub repository that provides example software for creating data products from popular InSAR processing software packages like GMT5SAR and ISCE as well as examples for reading and converting the data products into other formats. Digital object identifiers (DOI) have been incorporated into the InSAR archive allowing users to assign a permanent location for their processed result and easily reference the final data products. A metadata attribute is added to the HDF-EOS5 file when a DOI is minted for a data product. These data products are searchable through the SSARA federated query providing access to processed data for both expert and non-expert InSAR users. The archive facilitates timely distribution of processed data with particular importance for geohazards and event response.

Building Searchable Collections of Enterprise Speech Data.

ERIC Educational Resources Information Center

Cooper, James W.; Viswanathan, Mahesh; Byron, Donna; Chan, Margaret

The study has applied speech recognition and text-mining technologies to a set of recorded outbound marketing calls and analyzed the results. Since speaker-independent speech recognition technology results in a significantly lower recognition rate than that found when the recognizer is trained for a particular speaker, a number of post-processing…

Using JournalMap to improve ecological knowledge discovery and visualization

USDA-ARS?s Scientific Manuscript database

Background/Question/Methods Most of the ecological research conducted around the world is tied to specific places, however, that location information is locked up in the text and figures of scientific articles in myriad forms that are not easily searchable. While access to ecological literature ha...

78 FR 16456 - Service Obligations for Connect America Phase II and Determining Who Is an Unsubsidized Competitor

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-15

... account potential activities relating to education, health, employment, e-commerce, and civic engagement... methods: Federal eRulemaking Portal: http://www.regulations.gov . Follow the instructions for submitting... native format (e.g., .doc, .xml, .ppt, searchable .pdf). Participants in this proceeding should...

10 CFR 2.1013 - Use of the electronic docket during the proceeding.

Code of Federal Regulations, 2010 CFR

2010-01-01

... bi-tonal documents. (v) Electronic submissions must be generated in the appropriate PDF output format by using: (A) PDF—Formatted Text and Graphics for textual documents converted from native applications; (B) PDF—Searchable Image (Exact) for textual documents converted from scanned documents; and (C...

The Prospects for Security Sector Reform in Tunisia: A Year After the Revolution

DTIC Science & Technology

2012-09-01

included.86 This single, easily accessible, and searchable resource for all laws and amendments pertaining to the secu- rity sector greatly enhances ...Reform of the Peni - tentiary System,” Geneva Centre for the Democratic Control of Armed Forces, DCAF-Tunisie, October 5, 2011, available from dcaf

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

None Available

To make the web work better for science, OSTI has developed state-of-the-art technologies and services including a deep web search capability. The deep web includes content in searchable databases available to web users but not accessible by popular search engines, such as Google. This video provides an introduction to the deep web search engine.

DAM-ing the Digital Flood

ERIC Educational Resources Information Center

Raths, David

2008-01-01

With the widespread digitization of art, photography, and music, plus the introduction of streaming video, many colleges and universities are realizing that they must develop or purchase systems to preserve their school's digitized objects; that they must create searchable databases so that researchers can find and share copies of digital files;…

Using JournalMap to improve discovery and visualization of rangeland scientific knowledge

USDA-ARS?s Scientific Manuscript database

Most of the ecological research conducted around the world is tied to specific places; however, that location information is locked up in the text and figures of scientific articles in myriad forms that are not easily searchable. While access to ecological literature has improved dramatically in the...

Phytophthora-ID.org: A sequence-based Phytophthora identification tool

Treesearch

N.J. Grünwald; F.N. Martin; M.M. Larsen; C.M. Sullivan; C.M. Press; M.D. Coffey; E.M. Hansen; J.L. Parke

2010-01-01

Contemporary species identification relies strongly on sequence-based identification, yet resources for identification of many fungal and oomycete pathogens are rare. We developed two web-based, searchable databases for rapid identification of Phytophthora spp. based on sequencing of the internal transcribed spacer (ITS) or the cytochrome oxidase...

Information sources [Chapter 12

Treesearch

Daniel G. Neary; John N. Rinne; Alvin L. Medina

2012-01-01

The main information sources for the UVR consist of several web sites with general information and bibliographies. RMRS has publications on its Air, Water, Aquatic Environments (AWAE) Program Flagstaff web site. Another RMRS and University of Arizona website on semi-arid and arid watersheds contains a large, searchable bibliography of supporting information from the...

12 CFR 1235.4 - Minimum requirements of a record retention program.

Code of Federal Regulations, 2014 CFR

2014-01-01

... appropriate to support administrative, business, external and internal audit functions, and litigation of the... for appropriate back-up and recovery of electronic records to ensure the same accuracy as the primary... records, preferably searchable, must be maintained on immutable, non-rewritable storage in a manner that...

12 CFR 1235.4 - Minimum requirements of a record retention program.

Code of Federal Regulations, 2012 CFR

2012-01-01

... appropriate to support administrative, business, external and internal audit functions, and litigation of the... for appropriate back-up and recovery of electronic records to ensure the same accuracy as the primary... records, preferably searchable, must be maintained on immutable, non-rewritable storage in a manner that...

12 CFR 1235.4 - Minimum requirements of a record retention program.

Code of Federal Regulations, 2013 CFR

2013-01-01

... appropriate to support administrative, business, external and internal audit functions, and litigation of the... for appropriate back-up and recovery of electronic records to ensure the same accuracy as the primary... records, preferably searchable, must be maintained on immutable, non-rewritable storage in a manner that...

Effects of DDL Technology on Genre Learning

ERIC Educational Resources Information Center

Cotos, Elena; Link, Stephanie; Huffman, Sarah

2017-01-01

To better understand the promising effects of data-driven learning (DDL) on language learning processes and outcomes, this study explored DDL learning events enabled by the Research Writing Tutor (RWT), a web-based platform containing an English language corpus annotated to enhance rhetorical input, a concordancer that was searchable for…

Autonomous Language Learning on Twitter: Performing Affiliation with Target Language Users through #hashtags

ERIC Educational Resources Information Center

Solmaz, Osman

2017-01-01

The purpose of this study is to examine the potential of social networking sites for autonomous language learners, specifically the role of hashtag literacies in learners' affiliation performances with native speakers. Informed by ecological approach and guided by Zappavigna's (2012) concepts of "searchable talk" and "ambient…

CTD² Dashboard: a searchable web interface to connect validated results from the Cancer Target Discovery and Development Network* | Office of Cancer Genomics

Cancer.gov

The Cancer Target Discovery and Development (CTD2) Network aims to use functional genomics to accelerate the translation of high-throughput and high-content genomic and small-molecule data towards use in precision oncology.

Online Lab Books for Supervision of Project Students

ERIC Educational Resources Information Center

Badge, J. L.; Badge, R. M.

2009-01-01

In this article, the authors report a case study where Blackboard's wiki function was used to create electronic lab books for the supervision of undergraduate students completing laboratory based research projects. This successful experiment in supervision using electronic notebooks provided a searchable record of student work and a permanent…

Curriculum-based neurosurgery digital library.

PubMed

Langevin, Jean-Philippe; Dang, Thai; Kon, David; Sapo, Monica; Batzdorf, Ulrich; Martin, Neil

2010-11-01

Recent work-hour restrictions and the constantly evolving body of knowledge are challenging the current ways of teaching neurosurgery residents. To develop a curriculum-based digital library of multimedia content to face the challenges in neurosurgery education. We used the residency program curriculum developed by the Congress of Neurological Surgeons to structure the library and Microsoft Sharepoint as the user interface. This project led to the creation of a user-friendly and searchable digital library that could be accessed remotely and throughout the hospital, including the operating rooms. The electronic format allows standardization of the content and transformation of the operating room into a classroom. This in turn facilitates the implementation of a curriculum within the training program and improves teaching efficiency. Future work will focus on evaluating the efficacy of the library as a teaching tool for residents.

Nickel toxicity in the hepatopancreas of an isopod Porcellio scaber ( Oniscidea)

NASA Astrophysics Data System (ADS)

Tarnawska, M.; Migula, P.; Przybyłowicz, W.; Mesjasz-Przybyłowicz, J.; Augustyniak, M.

2007-07-01

This study is focused on recognizing how the functional role of hepatopancreas, the main metal storage organ in woodlice, is affected by the excess of nickel, a toxic element to soil invertebrates. Chronic Ni toxicity (24 weeks) was studied on four groups of woodlice kept on dry shredded maple leaves contaminated with Ni at average concentrations of 0.1 μg g -1 (control), 8.0 μg g -1 (Ni1), 75 μg g -1 (Ni2) and 270 μg g -1(Ni3) dry weight. Micro-PIXE mapping of elemental distribution in the hepatopancreas of the Porcellio scaber woodlice was used to study relations between nickel and other elements in individuals exposed to different metal concentrations in the diet. Data were processed using GeoPIXE II software. Transmission electron microscopy (TEM) was used to check the relations between ultrastructural changes in hepatopancreatic cells and nickel tissue burden. Elemental mapping showed a dose-related nickel bioaccumulation in the hepatopancreas at concentrations from 3 μg g -1 (uncontaminated control animals) to nearly 840 μg g -1 (Ni3). Generally, nickel was distributed uniformly in small aggregations. A combined evaluation of elemental maps and electronograms showed that aggregations of nickel in arbitrarily selected micro-areas in PIXE maps could be the granular structures observed in TEM electronograms. The mechanism of Ni sequestration in the hepatopancreas could be similar to this used for cadmium or lead. The sequences of ultrastructural changes, which follow the increased burdens of Ni in the hepatopancreatic cells, were: the increase of intracellular electron-dense granules, increase in the number of myelin-like structures, intensified mitochondrial swelling and appearance of concentrically arranged, rough endoplasmic reticulum.

Classification of Chemicals Based On Structured Toxicity ...

EPA Pesticide Factsheets

Thirty years and millions of dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data within the Toxicity Reference Database (ToxRefDB). Toxicity-based classifications of chemicals were performed as a model application of ToxRefDB. These endpoints will ultimately provide the anchoring toxicity information for the development of predictive models and biological signatures utilizing in vitro assay data. Utilizing query and structured data mining approaches, toxicity profiles were uniformly generated for greater than 300 chemicals. Based on observation rate, species concordance and regulatory relevance, individual and aggregated effects have been selected to classify the chemicals providing a set of predictable endpoints. ToxRefDB exhibits the utility of transforming unstructured toxicity data into structured data and, furthermore, into computable outputs, and serves as a model for applying such data to address modern toxicological problems.

Online Toxicity Monitors (OTM) for Distribution System Water Quality Monitoring

EPA Science Inventory

Drinking water distribution systems in the U.S. are vulnerable to episodic contamination events (both unintentional and intentional). The U.S. Environmental Protection Agency (EPA) is conducting research to investigate the use of broad-spectrum online toxicity monitors (OTMs) in ...

Accessibility, searchability, transparency and engagement of soil carbon data: The International Soil Carbon Network

NASA Astrophysics Data System (ADS)

Harden, Jennifer W.; Hugelius, Gustaf; Koven, Charlie; Sulman, Ben; O'Donnell, Jon; He, Yujie

2016-04-01

Soils are capacitors for carbon and water entering and exiting through land-atmosphere exchange. Capturing the spatiotemporal variations in soil C exchange through monitoring and modeling is difficult in part because data are reported unevenly across spatial, temporal, and management scales and in part because the unit of measure generally involves destructive harvest or non-recurrent measurements. In order to improve our fundamental basis for understanding soil C exchange, a multi-user, open source, searchable database and network of scientists has been formed. The International Soil Carbon Network (ISCN) is a self-chartered, member-based and member-owned network of scientists dedicated to soil carbon science. Attributes of the ISCN include 1) Targeted ISCN Action Groups which represent teams of motivated researchers that propose and pursue specific soil C research questions with the aim of synthesizing seminal articles regarding soil C fate. 2) Datasets to date contributed by institutions and individuals to a comprehensive, searchable open-access database that currently includes over 70,000 geolocated profiles for which soil C and other soil properties. 3) Derivative products resulting from the database, including depth attenuation attributes for C concentration and storage; C storage maps; and model-based assessments of emission/sequestration for future climate scenarios. Several examples illustrate the power of such a database and its engagement with the science community. First, a simplified, data-constrained global ecosystem model estimated a global sensitivity of permafrost soil carbon to climate change (g sensitivity) of -14 to -19 Pg C °C-1 of warming on a 100 years time scale. Second, using mathematical characterizations of depth profiles for organic carbon storage, C at the soil surface reflects Net Primary Production (NPP) and its allotment as moss or litter, while e-folding depths are correlated to rooting depth. Third, storage of deep C is highly correlated with bulk density and porosity of the rock/sediment matrix. Thus C storage is most stable at depth, yet is susceptible to changes in tillage, rooting depths, and erosion/sedimentation. Fourth, current ESMs likely overestimate the turnover time of soil organic carbon and subsequently overestimate soil carbon sequestration, thus datasets combined with other soil properties will help constrain the ESM predictions. Last, analysis of soil horizon and carbon data showed that soils with a history of tillage had significantly lower carbon concentrations in both near-surface and deep layers, and that the effect persisted even in reforested areas. In addition to the opportunities for empirical science using a large database, the database has great promise for evaluation of biogeochemical and earth system models. The preservation of individual soil core measurements avoids issues with spatial averaging while facilitating evaluation of advanced model processes such as depth distributions of soil carbon, land use impacts, and spatial heterogeneity.

41. DISCOVERY, SEARCH, AND COMMUNICATION OF TEXTUAL KNOWLEDGE RESOURCES IN DISTRIBUTED SYSTEMS a. Discovering and Utilizing Knowledge Sources for Metasearch Knowledge Systems

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

Zamora, Antonio

Advanced Natural Language Processing Tools for Web Information Retrieval, Content Analysis, and Synthesis. The goal of this SBIR was to implement and evaluate several advanced Natural Language Processing (NLP) tools and techniques to enhance the precision and relevance of search results by analyzing and augmenting search queries and by helping to organize the search output obtained from heterogeneous databases and web pages containing textual information of interest to DOE and the scientific-technical user communities in general. The SBIR investigated 1) the incorporation of spelling checkers in search applications, 2) identification of significant phrases and concepts using a combination of linguisticmore » and statistical techniques, and 3) enhancement of the query interface and search retrieval results through the use of semantic resources, such as thesauri. A search program with a flexible query interface was developed to search reference databases with the objective of enhancing search results from web queries or queries of specialized search systems such as DOE's Information Bridge. The DOE ETDE/INIS Joint Thesaurus was processed to create a searchable database. Term frequencies and term co-occurrences were used to enhance the web information retrieval by providing algorithmically-derived objective criteria to organize relevant documents into clusters containing significant terms. A thesaurus provides an authoritative overview and classification of a field of knowledge. By organizing the results of a search using the thesaurus terminology, the output is more meaningful than when the results are just organized based on the terms that co-occur in the retrieved documents, some of which may not be significant. An attempt was made to take advantage of the hierarchy provided by broader and narrower terms, as well as other field-specific information in the thesauri. The search program uses linguistic morphological routines to find relevant entries regardless of whether terms are stored in singular or plural form. Implementation of additional inflectional morphology processes for verbs can enhance retrieval further, but this has to be balanced by the possibility of broadening the results too much. In addition to the DOE energy thesaurus, other sources of specialized organized knowledge such as the Medical Subject Headings (MeSH), the Unified Medical Language System (UMLS), and Wikipedia were investigated. The supporting role of the NLP thesaurus search program was enhanced by incorporating spelling aid and a part-of-speech tagger to cope with misspellings in the queries and to determine the grammatical roles of the query words and identify nouns for special processing. To improve precision, multiple modes of searching were implemented including Boolean operators, and field-specific searches. Programs to convert a thesaurus or reference file into searchable support files can be deployed easily, and the resulting files are immediately searchable to produce relevance-ranked results with builtin spelling aid, morphological processing, and advanced search logic. Demonstration systems were built for several databases, including the DOE energy thesaurus.« less

Distribution of toxic alkaloids in tissues from three herbal medicine Aconitum species using laser micro-dissection, UHPLC-QTOF MS and LC-MS/MS techniques.

PubMed

Jaiswal, Yogini; Liang, Zhitao; Ho, Alan; Wong, LaiLai; Yong, Peng; Chen, Hubiao; Zhao, Zhongzhen

2014-11-01

Aconite poisoning continues to be a major type of poisoning caused by herbal drugs in many countries. Nevertheless, despite its toxic characteristics, aconite is used because of its valuable therapeutic benefits. The aim of the present study was to determine the distribution of toxic alkaloids in tissues of aconite roots through chemical profiling. Three species were studied, all being used in traditional Chinese Medicine (TCM) and traditional Indian medicine (Ayurveda), namely: Aconitum carmichaelii, Aconitum kusnezoffii and Aconitum heterophyllum. Laser micro-dissection was used for isolation of target microscopic tissues, such as the metaderm, cortex, xylem, pith, and phloem, with ultra-high performance liquid chromatography equipped with quadrupole time-of-flight mass spectrometry (UHPLC-QTOF MS) employed for detection of metabolites. Using a multi-targeted approach through auto and targeted LC-MS/MS, 48 known compounds were identified and the presence of aconitine, mesaconitine and hypaconitine that are the biomarkers of this plant was confirmed in the tissues. These results suggest that the three selected toxic alkaloids were exclusively found in A. carmichaelii and A. kusnezoffii. The most toxic components were found in large A. carmichaelii roots with more lateral root projections, and specifically in the metaderm, cork and vascular bundle tissues. The results from metabolite profiling were correlated with morphological features to predict the tissue specific distribution of toxic components and toxicity differences among the selected species. By careful exclusion of tissues having toxic diester diterpenoid alkaloids, the beneficial effects of aconite can still be retained and the frequency of toxicity occurrences can be greatly reduced. Knowledge of tissue-specific metabolite distribution can guide users and herbal drug manufacturers in prudent selection of relatively safer and therapeutically more effective parts of the root. The information provided from this study can contribute towards improved and effective management of therapeutically important, nonetheless, toxic drug such as Aconite. Copyright © 2014 Elsevier Ltd. All rights reserved.

Analysis of sublethal arsenic toxicity to Ceratophyllum demersum: subcellular distribution of arsenic and inhibition of chlorophyll biosynthesis

PubMed Central

Mishra, Seema; Alfeld, Matthias; Sobotka, Roman; Andresen, Elisa; Falkenberg, Gerald; Küpper, Hendrik

2016-01-01

Arsenic (As) pollution is a serious concern worldwide. Recent studies under environmentally relevant conditions revealed that, in the aquatic plant Ceratophyllum demersum, pigments are the first observable target of toxicity, prior to any effect on photosynthetic parameters or to oxidative stress. Lethal toxicity was initiated by a change of As species and their distribution pattern in various tissues. Here, the localization of As was investigated at the subcellular level through X-ray fluorescence using a submicron beam and a Maia detector. Further, it was possible to obtain useful tissue structural information from the ratio of the tomogram of photon flux behind the sample to the tomogram of Compton scattering. The micro-X-ray fluorescence tomograms showed that As predominantly accumulated in the nucleus of the epidermal cells in young mature leaves exposed to sublethal 1 µM As. This suggests that As may exert toxic effects in the nucleus, for example, by interfering with nucleic acid synthesis by replacing phosphorous with As. At higher cellular concentrations, As was mainly stored in the vacuole, particularly in mature leaves. An analysis of precursors of chlorophyll and degradation metabolites revealed that the observed decrease in chlorophyll concentration was associated with hindered biosynthesis, and was not due to degradation. Coproporphyrinogen III could not be detected after exposure to only 0.5 µM As. Levels of subsequent precursors, for example, protoporphyrin IX, Mg-protoporphyrin, Mg-protoporphyrin methyl ester, and divinyl protochlorophyllide, were significantly decreased at this concentration as well, indicating that the pathway was blocked upstream of tetrapyrrole synthesis. PMID:27340233

Unwrapping 3D complex hollow organs for spatial dose surface analysis.

PubMed

Witztum, A; George, B; Warren, S; Partridge, M; Hawkins, M A

2016-11-01

Toxicity dose-response models describe the correlation between dose delivered to an organ and a given toxic endpoint. Duodenal toxicity is a dose limiting factor in the treatment of pancreatic cancer with radiation but the relationship between dose and toxicity in the duodenum is not well understood. While there have been limited studies into duodenal toxicity through investigations of the volume of the organ receiving dose over a specific threshold, both dose-volume and dose-surface histograms lack spatial information about the dose distribution, which may be important in determining normal tissue response. Due to the complex geometry of the duodenum, previous methods for unwrapping tubular organs for spatial modeling of toxicity are insufficient. A geometrically robust method for producing 2D dose surface maps (DSMs), specifically for the duodenum, has been developed and tested in order to characterize the spatial dose distribution. The organ contour is defined using Delaunay triangulation. The user selects a start and end coordinate in the structure and a path is found by regulating both length and curvature. This path is discretized and rays are cast from each point on the plane normal to the vector between the previous and the next point on the path and the dose at the closest perimeter point recorded. These angular perimeter slices are "unwrapped" from the edge distal to the pancreas to ensure the high dose region (proximal to the tumor) falls in the centre of the dose map. Gamma analysis is used to quantify the robustness of this method and the effect of overlapping planes. This method was used to extract DSMs for 15 duodena, with one esophagus case to illustrate the application to simpler geometries. Visual comparison indicates that a 30 × 30 map provides sufficient resolution to view gross spatial features of interest. A lookup table is created to store the area (cm 2 ) represented by each pixel in the DSMs in order to allow spatial descriptors in absolute size. The method described in this paper is robust, requires minimal human interaction, has been shown to be generalizable to simpler geometries, and uses readily available commercial software. The difference seen in DSMs due to overlapping planes is large and justifies the need for a solution that removes such planes. This is the first time 2D dose surface maps have been produced for the duodenum and provide spatial dose distribution information which can be explored to create models that may improve toxicity prediction in treatments for locally advanced pancreatic cancer.

Earthspace: A National Clearinghouse For Higher Education In Space And Earth Sciences

NASA Astrophysics Data System (ADS)

CoBabe-Ammann, Emily; Shipp, S.; Dalton, H.

2012-10-01

The EarthSpace is a searchable database of undergraduate classroom materials for undergraduate faculty teaching earth and space sciences at both the introductory and upper division levels. Modeled after the highly successful SERC clearinghouse for geosciences assets, EarthSpace was designed for easy submission of classroom assets - from homeworks and computerinteractives to laboratories and demonstrations. All materials are reviewedbefore posting, and authors adhere to the Creative Commons Non-Commercial Attribution (CC-BY NC 3.0). If authors wish, their EarthSpace materials are automatically cross-posted to other digital libraries (e.g., ComPADRE) and virtual higher education communities(e.g., Connexions). As new electronic repositories come online, EarthSpace materials will automatically be sent. So faculty submit their materials only once and EarthSpace ensures continual distribution as time goes on and new opportunities arise. In addition to classroom materials, EarthSpace provides news and information about educational research and best practices, funding opportunities, and ongoing efforts and collaborations for undergraduate education. http://www.lpi.usra.edu/earthspace

Annotated catalog and bibliography of the cyclocephaline scarab beetles (Coleoptera, Scarabaeidae, Dynastinae, Cyclocephalini).

PubMed

Moore, Matthew R; Cave, Ronald D; Branham, Marc A

2018-01-01

Cyclocephaline scarab beetles represent the second largest tribe of the subfamily Dynastinae, and the group includes the most speciose genus of dynastines, Cyclocephala . The period following publication of Sebő Endrődi's The Dynastinae of the World has seen a huge increase in research interest on cyclocephalines, and much of this research has not been synthesized. The objective of this catalog and bibliography is to compile an exhaustive list of taxa in Cyclocephalini. This paper provides an updated foundation for understanding the taxonomy and classification of 14 genera and over 500 species in the tribe. It discusses the history of cataloging dynastine species, clarifies issues surrounding the neotype designations in Endrődi's revision of Cyclocephalini, synthesizes all published distribution data for cyclocephaline species, and increases accessibility to the voluminous literature on the group by providing an easily searchable bibliography for each species. We propose the nomen novum Cyclocephala rogerpauli , new replacement name , for C. nigra Dechambre.

Annotated catalog and bibliography of the cyclocephaline scarab beetles (Coleoptera, Scarabaeidae, Dynastinae, Cyclocephalini)

PubMed Central

Moore, Matthew R.; Cave, Ronald D.; Branham, Marc A.

2018-01-01

Abstract Cyclocephaline scarab beetles represent the second largest tribe of the subfamily Dynastinae, and the group includes the most speciose genus of dynastines, Cyclocephala. The period following publication of Sebő Endrődi’s The Dynastinae of the World has seen a huge increase in research interest on cyclocephalines, and much of this research has not been synthesized. The objective of this catalog and bibliography is to compile an exhaustive list of taxa in Cyclocephalini. This paper provides an updated foundation for understanding the taxonomy and classification of 14 genera and over 500 species in the tribe. It discusses the history of cataloging dynastine species, clarifies issues surrounding the neotype designations in Endrődi’s revision of Cyclocephalini, synthesizes all published distribution data for cyclocephaline species, and increases accessibility to the voluminous literature on the group by providing an easily searchable bibliography for each species. We propose the nomen novum Cyclocephala rogerpauli, new replacement name, for C. nigra Dechambre. PMID:29670449

Increased Fire and Toxic Contaminant Detection Responsibility by Use of Distributed, Aspirating Sensors

NASA Technical Reports Server (NTRS)

Youngblood, Wallace W.

1990-01-01

Viewgraphs of increased fire and toxic contaminant detection responsivity by use of distributed, aspirating sensors for space station are presented. Objectives of the concept described are (1) to enhance fire and toxic contaminant detection responsivity in habitable regions of space station; (2) to reduce system weight and complexity through centralized detector/monitor systems; (3) to increase fire signature information from selected locations in a space station module; and (4) to reduce false alarms.

Using sheep genomes from diverse U.S. breeds to identify missense variants in genes affecting fecundity

USDA-ARS?s Scientific Manuscript database

Background: Access to sheep genome sequences significantly improves the chances of identifying genes that may influence the health, welfare, and productivity of these animals. Methods: A public, searchable DNA sequence resource for U.S. sheep was created with whole genome sequence (WGS) of 96 rams. ...

49 CFR 573.15 - Public Availability of Motor Vehicle Recall Information.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Internet. The information shall be in a format that is searchable by vehicle make and model and vehicle... following requirements: (1) Be free of charge and not require users to register or submit information, other... (Internet link) to it conspicuously placed on the manufacturer's main United States' Web page; (3) Not...

49 CFR 573.15 - Public availability of motor vehicle recall information.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Internet. The information shall be in a format that is searchable by vehicle make and model and vehicle... following requirements: (1) Be free of charge and not require users to register or submit information, other... (Internet link) to it conspicuously placed on the manufacturer's main United States' Web page; (3) Not...

Deep Web video

ScienceCinema

None Available

2018-02-06

To make the web work better for science, OSTI has developed state-of-the-art technologies and services including a deep web search capability. The deep web includes content in searchable databases available to web users but not accessible by popular search engines, such as Google. This video provides an introduction to the deep web search engine.

76 FR 81990 - 2002 Reopened-Previously Denied Determinations; Notice of Negative Determinations on...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-29

... reconsideration investigation revealed that the following workers groups have not met the certification criteria... Myers, FL. TA-W-80,026; Computer Task Group, Mechanicsburg, PA. TA-W-80,047; Cenveo, Inc., Springfield... Department's Web site at tradeact/taa/taa--search--form.cfm under the searchable listing of determinations or...

76 FR 76189 - 2002 Reopened-Previously Denied Determinations; Notice of Revised Denied Determinations on...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-12-06

... reconsideration investigation revealed that the following workers groups have met the certification criteria under... Salt Lake City, UT: March 24, 2010. TA-W-80,153; Intercontinental Hotels Group, Alpharetta, GA: May 4... available on the Department's Web site at tradeact/taa/taa-- search--form.cfm under the searchable listing...

39 CFR 3007.10 - Submission of non-public materials under seal.

Code of Federal Regulations, 2010 CFR

2010-07-01

...-public materials shall submit two copies consisting, where practicable, of two paper hard copies as well... available PC application. Each page of any paper hard copy non-public materials submitted shall be clearly... submitted in a searchable electronic format, but need not be submitted in its native format. As part of its...

State Energy Efficiency Program Evaluation Inventory

EIA Publications

2013-01-01

The focus of this inventory, some of which has been placed into a searchable spreadsheet, is to support the National Energy Modeling System (NEMS) and to research cost information in state-mandated energy efficiency program evaluations – e.g., for use in updating analytic and modeling assumptions used by the U.S. Energy Information Administration (EIA).

Document Classification in Support of Automated Metadata Extraction Form Heterogeneous Collections

ERIC Educational Resources Information Center

Flynn, Paul K.

2014-01-01

A number of federal agencies, universities, laboratories, and companies are placing their documents online and making them searchable via metadata fields such as author, title, and publishing organization. To enable this, every document in the collection must be catalogued using the metadata fields. Though time consuming, the task of identifying…

Patent Databases. . .A Survey of What Is Available from DIALOG, Questel, SDC, Pergamon and INPADOC.

ERIC Educational Resources Information Center

Kulp, Carol S.

1984-01-01

Presents survey of two groups of databases covering patent literature: patent literature only and general literature that includes patents relevant to subject area of database. Description of databases and comparison tables for patent and general databases (cost, country coverage, years covered, update frequency, file size, and searchable data…

The Exercise: An Exercise Generator Tool for the SOURCe Project

ERIC Educational Resources Information Center

Kakoyianni-Doa, Fryni; Tziafa, Eleni; Naskos, Athanasios

2016-01-01

The Exercise, an Exercise generator in the SOURCe project, is a tool that complements the properties and functionalities of the SOURCe project, which includes the search engine for the Searchable Online French-Greek parallel corpus for the UniveRsity of Cyprus (SOURCe) (Kakoyianni-Doa & Tziafa, 2013), the PENCIL (an alignment tool)…

76 FR 71267 - Standardized and Enhanced Disclosure Requirements for Television Broadcast Licensee Public...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-11-17

... collect and publish data in forms that make it easy for citizens, entrepreneurs, software developers, and... serves the public interest easier to understand and more accessible will not only promote discussion... order to create a permanent, searchable record of these arrangements and afford easy access by consumers...

Re-Framing Teacher Evaluation Discourse in the Media: An Analysis and Narrative-Based Proposal

ERIC Educational Resources Information Center

Ulmer, Jasmine B.

2016-01-01

Recent publications by major newspapers in the USA have reinforced the perception that teacher quality represents a national crisis. By releasing individual teacher evaluation data in online, searchable databases, several newspapers have influenced public perceptions of teachers and teaching. A framing analysis of selected media events and…

Alaska Department of Natural Resources

Science.gov Websites

/08/2018 First Day Hikes planned in Delta Junction, Homer, Sitka, Ketchikan, and Juneau 12/27/2017 searchable online tool 07/31/2017 Contracts awarded for private operation of Delta Area state parks 07/31 Outdoor Recreation Director 07/06/2017 State seeks private contractors to operate Delta Area state parks

Using an online genome resource to identify myostatin variation in U.S. sheep

USDA-ARS?s Scientific Manuscript database

We created a public, searchable DNA sequence resource for sheep that contained approximately 14x whole genome sequence of 96 rams. The animals represent 10 popular U.S. breeds and share minimal pedigree relationships, making the resource suitable for viewing gene variants in the user-friendly Integ...

University Real Estate Development Database: A Database-Driven Internet Research Tool

ERIC Educational Resources Information Center

Wiewel, Wim; Kunst, Kara

2008-01-01

The University Real Estate Development Database is an Internet resource developed by the University of Baltimore for the Lincoln Institute of Land Policy, containing over six hundred cases of university expansion outside of traditional campus boundaries. The University Real Estate Development database is a searchable collection of real estate…

Short guide to SDI profiling at ORNL

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

Pomerance, H.S.

1976-06-01

ORNL has machine-searchable data bases that correspond to printed indexes and abstracts. This guide describes the peculiarities of those several data bases and the conventions of the ORNL search system so that users can write their own queries or search profiles and can interpret the part of the output that is encoded.

Perceived Factors Influencing Instructors' Use of E-Textbooks in Higher Education

ERIC Educational Resources Information Center

Wang, Sirui; Hartsell, Taralynn

2017-01-01

As a form of digital content, e-Textbooks make learning content portable, transferable, and searchable. Such technology increases students' engagement in learning and make learning highly interactive. However, the adoption of using e-Textbooks in higher education is far from its confirmation stage. This study examines the relationship between…

Host and habitat index for Phytophthora species in Oregon

Treesearch

Everett Hansen; Paul Reeser; Wendy Sutton; Laura Sims

2012-01-01

In this contribution we compile existing records from available sources of reliably identified Phytophthora species from forests and forest trees in Oregon, USA. A searchable version of this information may be found in the Forest Phytophthoras of the World Disease Finder (select USA-Oregon). We have included isolations from soil and streams in...

Kratylos: A Tool for Sharing Interlinearized and Lexical Data in Diverse Formats

ERIC Educational Resources Information Center

Kaufman, Daniel; Finkel, Raphael

2018-01-01

In this paper we present Kratylos, at www.kratylos.org/, a web application that creates searchable multimedia corpora from data collections in diverse formats, including collections of interlinearized glossed text (IGT) and dictionaries. There exists a crucial lacuna in the electronic ecology that supports language documentation and linguistic…

Contact Us about NREL | NREL

Science.gov Websites

Contact Us about NREL Contact Us about NREL Find mailing addresses, phone numbers, and contact -2157 202-488-2200 Phone Phone Numbers View a list of important phone numbers. Address book Contact a Staff Member at NREL Our searchable staff directory has contact information for staff. Questions

Digital London: Creating a Searchable Web of Interlinked Sources on Eighteenth Century London

ERIC Educational Resources Information Center

Shoemaker, Robert

2005-01-01

Purpose: To outline the conceptual and technical difficulties encountered, as well as the opportunities created, when developing an interlinked collection of web-based digitised primary sources on eighteenth century London. Design/methodology/approach: As a pilot study for a larger project, a variety of primary sources, including the "Old…

GEONETCast Americas

Science.gov Websites

unless the user has internet access on the same machine. The products, including metadata, that are on is an access portal to GEONETCast products. It is a searchable database that can be found at -channel. This version will run on a local computer at a user site but internet links will not function

Indexed Captioned Searchable Videos: A Learning Companion for STEM Coursework

ERIC Educational Resources Information Center

Tuna, Tayfun; Subhlok, Jaspal; Barker, Lecia; Shah, Shishir; Johnson, Olin; Hovey, Christopher

2017-01-01

Videos of classroom lectures have proven to be a popular and versatile learning resource. A key shortcoming of the lecture video format is accessing the content of interest hidden in a video. This work meets this challenge with an advanced video framework featuring topical indexing, search, and captioning (ICS videos). Standard optical character…

iLOG: A Framework for Automatic Annotation of Learning Objects with Empirical Usage Metadata

ERIC Educational Resources Information Center

Miller, L. D.; Soh, Leen-Kiat; Samal, Ashok; Nugent, Gwen

2012-01-01

Learning objects (LOs) are digital or non-digital entities used for learning, education or training commonly stored in repositories searchable by their associated metadata. Unfortunately, based on the current standards, such metadata is often missing or incorrectly entered making search difficult or impossible. In this paper, we investigate…

Partner Resources at CBE

Science.gov Websites

Resources CBE's Next Industry Advisor Board Meeting CBE's Industry Advisory Board (IAB) provides guidance meeting logistics page >> Partner Website We maintain a website that allows partner access to all searchable by keyword and author on the eRepository, a service of the California Digital Library. Go to CBE

Digging Deeper: The Deep Web.

ERIC Educational Resources Information Center

Turner, Laura

2001-01-01

Focuses on the Deep Web, defined as Web content in searchable databases of the type that can be found only by direct query. Discusses the problems of indexing; inability to find information not indexed in the search engine's database; and metasearch engines. Describes 10 sites created to access online databases or directly search them. Lists ways…

[Systematic literature search in PubMed : A short introduction].

PubMed

Blümle, A; Lagrèze, W A; Motschall, E

2018-03-01

In order to identify current (and relevant) evidence for a specific clinical question within the unmanageable amount of information available, solid skills in performing a systematic literature search are essential. An efficient approach is to search a biomedical database containing relevant literature citations of study reports. The best known database is MEDLINE, which is searchable for free via the PubMed interface. In this article, we explain step by step how to perform a systematic literature search via PubMed by means of an example research question in the field of ophthalmology. First, we demonstrate how to translate the clinical problem into a well-framed and searchable research question, how to identify relevant search terms and how to conduct a text word search and a search with keywords in medical subject headings (MeSH) terms. We then show how to limit the number of search results if the search yields too many irrelevant hits and how to increase the number in the case of too few citations. Finally, we summarize all essential principles that guide a literature search via PubMed.

An Efficient Quantum Somewhat Homomorphic Symmetric Searchable Encryption

NASA Astrophysics Data System (ADS)

Sun, Xiaoqiang; Wang, Ting; Sun, Zhiwei; Wang, Ping; Yu, Jianping; Xie, Weixin

2017-04-01

In 2009, Gentry first introduced an ideal lattices fully homomorphic encryption (FHE) scheme. Later, based on the approximate greatest common divisor problem, learning with errors problem or learning with errors over rings problem, FHE has developed rapidly, along with the low efficiency and computational security. Combined with quantum mechanics, Liang proposed a symmetric quantum somewhat homomorphic encryption (QSHE) scheme based on quantum one-time pad, which is unconditional security. And it was converted to a quantum fully homomorphic encryption scheme, whose evaluation algorithm is based on the secret key. Compared with Liang's QSHE scheme, we propose a more efficient QSHE scheme for classical input states with perfect security, which is used to encrypt the classical message, and the secret key is not required in the evaluation algorithm. Furthermore, an efficient symmetric searchable encryption (SSE) scheme is constructed based on our QSHE scheme. SSE is important in the cloud storage, which allows users to offload search queries to the untrusted cloud. Then the cloud is responsible for returning encrypted files that match search queries (also encrypted), which protects users' privacy.

English semantic word-pair norms and a searchable Web portal for experimental stimulus creation.

PubMed

Buchanan, Erin M; Holmes, Jessica L; Teasley, Marilee L; Hutchison, Keith A

2013-09-01

As researchers explore the complexity of memory and language hierarchies, the need to expand normed stimulus databases is growing. Therefore, we present 1,808 words, paired with their features and concept-concept information, that were collected using previously established norming methods (McRae, Cree, Seidenberg, & McNorgan Behavior Research Methods 37:547-559, 2005). This database supplements existing stimuli and complements the Semantic Priming Project (Hutchison, Balota, Cortese, Neely, Niemeyer, Bengson, & Cohen-Shikora 2010). The data set includes many types of words (including nouns, verbs, adjectives, etc.), expanding on previous collections of nouns and verbs (Vinson & Vigliocco Journal of Neurolinguistics 15:317-351, 2008). We describe the relation between our and other semantic norms, as well as giving a short review of word-pair norms. The stimuli are provided in conjunction with a searchable Web portal that allows researchers to create a set of experimental stimuli without prior programming knowledge. When researchers use this new database in tandem with previous norming efforts, precise stimuli sets can be created for future research endeavors.

Analysis and prediction of structure-reactive toxicity relationships of substituted aromatic compounds

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

Liu, Z.T.; Wang, L.S.; Chen, S.P.

1996-12-31

The fundamental differentiation of toxicity is between reactive and nonreactive toxicity. Reactive toxicity is associated with a specific mechanism for the reaction with an enzyme or inhibition of a metabolic pathway, and nonreactive toxicity is related directly to the quantity of toxicant acting upon the cell. The quantitative structure-activity relationships (QSARs) have been successfully used in the nonreactive toxicity, such as prediction of the toxicity of nonreactive compounds based on their solubility in the lipids of organisms. The elements of molecular structure that are most closely related to nonreactive toxicity are those that describe the partitioning of the toxicant intomore » the organism, while QSARs for the reactive toxicity are less common in the environmental toxicology literature. With the recent increase in the use of synthetic substituted benzenes as industrial chemicals, the accurate analysis of the effect of reactive toxic chemicals has become recognized with QSAR. For this purpose, we selected the fish (Carassias auratus) as the test organism, measured the acute toxicity of 50% lethal concentration (LC{sub 50}) of the chemicals and the adenosine triphosphate (ATP) content of the liver cells for the organism. These determined the relationships of the acute toxicity of some substituted benzenes with their physicochemical structural parameters. The effects on the ATP content was also compared to predict biological reactivities of the chemicals, so as to find some clues to explain the mode of mechanism of the toxicity. 17 refs., 1 tab.« less

Inclusion of dosimetric data as covariates in toxicity-related radiogenomic studies : A systematic review.

PubMed

Yahya, Noorazrul; Chua, Xin-Jane; Manan, Hanani A; Ismail, Fuad

2018-05-17

This systematic review evaluates the completeness of dosimetric features and their inclusion as covariates in genetic-toxicity association studies. Original research studies associating genetic features and normal tissue complications following radiotherapy were identified from PubMed. The use of dosimetric data was determined by mining the statement of prescription dose, dose fractionation, target volume selection or arrangement and dose distribution. The consideration of the dosimetric data as covariates was based on the statement mentioned in the statistical analysis section. The significance of these covariates was extracted from the results section. Descriptive analyses were performed to determine their completeness and inclusion as covariates. A total of 174 studies were found to satisfy the inclusion criteria. Studies published ≥2010 showed increased use of dose distribution information (p = 0.07). 33% of studies did not include any dose features in the analysis of gene-toxicity associations. Only 29% included dose distribution features as covariates and reported the results. 59% of studies which included dose distribution features found significant associations to toxicity. A large proportion of studies on the correlation of genetic markers with radiotherapy-related side effects considered no dosimetric parameters. Significance of dose distribution features was found in more than half of the studies including these features, emphasizing their importance. Completeness of radiation-specific clinical data may have increased in recent years which may improve gene-toxicity association studies.

Changes in subcellular distribution and antioxidant compounds involved in Pb accumulation and detoxification in Neyraudia reynaudiana.

PubMed

Zhou, Chuifan; Huang, Meiying; Li, Ying; Luo, Jiewen; Cai, Li Ping

2016-11-01

The effects of increasing concentrations of lead (Pb) on Pb accumulation, subcellular distribution, ultrastructure, photosynthetic characteristics, antioxidative enzyme activity, malondialdehyde content, and phytochelatin contents were investigated in Neyraudia reynaudiana seedlings after a 21-day exposure. A Pb analysis at the subcellular level showed that the majority of Pb in the roots was associated with the cell wall fraction, followed by the soluble fraction. In contrast, the majority of the Pb in the leaves was located in the soluble fraction based on transmission electron microscopy and energy dispersive X-ray analyses. Furthermore, high Pb concentrations adversely affected N. reynaudiana cellular structure. The changes in enzyme activity suggested that the antioxidant system plays an important role in eliminating or alleviating Pb toxicity, both in the roots and leaves of N. reynaudiana. Additionally, the phytochelatin contents in the roots and leaves differed significantly between Pb-spiked treatments and control plants. Our results provide strong evidence that cell walls restrict Pb uptake into the protoplasm and establish an important protective barrier. Subsequent vacuolar compartmentalization in leaves could isolate Pb from other substances in the cell and minimize Pb toxicity in other organelles over time. These results also demonstrated that the levels of antioxidant enzymes and phytochelatin in leaves and roots are correlated with Pb toxicity. These detoxification mechanisms promote Pb tolerance in N. reynaudiana.

Lolitrem B and Indole Diterpene Alkaloids Produced by Endophytic Fungi of the Genus Epichloë and Their Toxic Effects in Livestock.

PubMed

Philippe, Guerre

2016-02-15

Different group of alkaloids are produced during the symbiotic development of fungal endophytes of the genus Epichloë in grass. The structure and toxicity of the compounds vary considerably in mammalian herbivores and in crop pests. Alkaloids of the indole-diterpene group, of which lolitrem B is the most toxic, were first characterized in endophyte-infected perennial ryegrass, and are responsible for "ryegrass staggers." Ergot alkaloids, of which ergovaline is the most abundant ergopeptide alkaloid produced, are also found in ryegrass, but generally at a lower rate than lolitrem B. Other alkaloids such as lolines and peramine are toxic for crop pests but have weak toxicological properties in mammals. The purpose of this review is to present indole-diterpene alkaloids produced in endophyte infected ryegrass from the first characterization of ryegrass staggers to the determination of the toxicokinetics of lolitrem B and of their mechanism of action in mammals, focusing on the different factors that could explain the worldwide distribution of the disease. Other indole diterpene alkaloids than lolitrem B that can be found in Epichloë infected ryegrass, and their tremorgenic properties, are presented in the last section of this review.

USE OF MULTI-PHOTON LASER-SCANNING MICROSCOPY TO DESCRIBE THE DISTRIBUTION OF XENOBIOTIC CHEMICALS IN FISH EARLY LIFE STAGES

EPA Science Inventory

To better understand the mechanisms by which persistent bioaccumulative toxicants (PBTs) produce toxicity during fish early life stages (ELS), dose response relationships need to be determined in relation to the dynamic distribution of chemicals in sensitive tissues. In this stud...

TIPdb: a database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan.

PubMed

Lin, Ying-Chi; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng; Tung, Chun-Wei

2013-01-01

The unique geographic features of Taiwan are attributed to the rich indigenous and endemic plant species in Taiwan. These plants serve as resourceful bank for biologically active phytochemicals. Given that these plant-derived chemicals are prototypes of potential drugs for diseases, databases connecting the chemical structures and pharmacological activities may facilitate drug development. To enhance the utility of the data, it is desirable to develop a database of chemical compounds and corresponding activities from indigenous plants in Taiwan. A database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan was constructed. The database, TIPdb, is composed of a standardized format of published anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. A browse function was implemented for users to browse the database in a taxonomy-based manner. Search functions can be utilized to filter records of interest by botanical name, part, chemical class, or compound name. The structured and searchable database TIPdb was constructed to serve as a comprehensive and standardized resource for anticancer, antiplatelet, and antituberculosis compounds search. The manually curated chemical structures and activities provide a great opportunity to develop quantitative structure-activity relationship models for the high-throughput screening of potential anticancer, antiplatelet, and antituberculosis drugs.

TIPdb: A Database of Anticancer, Antiplatelet, and Antituberculosis Phytochemicals from Indigenous Plants in Taiwan

PubMed Central

Lin, Ying-Chi; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng; Tung, Chun-Wei

2013-01-01

The unique geographic features of Taiwan are attributed to the rich indigenous and endemic plant species in Taiwan. These plants serve as resourceful bank for biologically active phytochemicals. Given that these plant-derived chemicals are prototypes of potential drugs for diseases, databases connecting the chemical structures and pharmacological activities may facilitate drug development. To enhance the utility of the data, it is desirable to develop a database of chemical compounds and corresponding activities from indigenous plants in Taiwan. A database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan was constructed. The database, TIPdb, is composed of a standardized format of published anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. A browse function was implemented for users to browse the database in a taxonomy-based manner. Search functions can be utilized to filter records of interest by botanical name, part, chemical class, or compound name. The structured and searchable database TIPdb was constructed to serve as a comprehensive and standardized resource for anticancer, antiplatelet, and antituberculosis compounds search. The manually curated chemical structures and activities provide a great opportunity to develop quantitative structure-activity relationship models for the high-throughput screening of potential anticancer, antiplatelet, and antituberculosis drugs. PMID:23766708

STRUCTURE-ACTIVITY APPROACHES AND DATA EXPLORATION TOOLS FOR PRIORITIZING AND ASSESSING THE TOXICITY OF HAZARDOUS AIR POLLUTANTS

EPA Science Inventory

STRUCTURE-ACTIVITY APPROACHES AND DATA EXPLORATION TOOLS FOR PRIORITIZING AND ASSESSING THE TOXICITY OF HAZARDOUS AIR POLLUTANTS

Hazardous Air Pollutants (HAPs) refers to a set of structurally diverse environmental chemicals, many with limited toxicity data, that have...

Design of a Recommendation System for Adding Support in the Treatment of Chronic Patients.

PubMed

Torkar, Simon; Benedik, Peter; Rajkovič, Uroš; Šušteršič, Olga; Rajkovič, Vladislav

2016-01-01

Rapid growth of chronic disease cases around the world is adding pressure on healthcare providers to ensure a structured patent follow-up during chronic disease management process. In response to the increasing demand for better chronic disease management and improved health care efficiency, nursing roles have been specialized or enhanced in the primary health care setting. Nurses become key players in chronic disease management process. Study describes a system to help nurses manage the care process of patient with chronic disease. It supports focusing nurse's attention on those resources/solutions that are likely to be most relevant to their particular situation/problem in nursing domain. System is based on multi-relational property graph representing a flexible modeling construct. Graph allows modeling a nursing ontology and the indices that partition domain into an efficient, searchable space where the solution to a problem is seen as abstractly defined traversals through its vertices and edges.

Probabilistic risk assessment of cotton pyrethroids: I. Distributional analyses of laboratory aquatic toxicity data.

PubMed

Solomon, K R; Giddings, J M; Maund, S J

2001-03-01

This is the first in a series of five papers that assess the risk of the cotton pyrethroids in aquatic ecosystems in a series of steps ranging from the analysis of effects data through modeling exposures in the landscape. Pyrethroid insecticides used on cotton have the potential to contaminate aquatic systems. The objectives of this study were to develop probabilistic estimates of toxicity distributions, to compare these among the pyrethroids, and to evaluate cypermethrin as a representative pyrethroid for the purposes of a class risk assessment of the pyrethroids. The distribution of cypermethrin acute toxicity data gave 10th centile values of 10 ng/L for all organisms, 6.4 ng/L for arthropods, and 380 ng/L for vertebrates. For bifenthrin, cyfluthrin, lambda-cyhalothrin, and deltamethrin, the 10th centile values for all organisms were 15, 12, 10, and 9 ng/L, respectively, indicating similar or somewhat lower toxicity than cypermethrin. For tralomethrin and fenpropathrin, the 10th centiles were <310 and 240 ng/L, respectively. The distribution of permethrin toxicity to all organisms, arthropods, and vertebrates gave 10th centiles of 180, 76, and 1600 ng/L, respectively, whereas those for fenvalerate were 37, 8, and 150 ng/L. With the exception of tralomethrin, the distributions of acute toxicity values had similar slopes, suggesting that the variation of sensitivity in a range of aquatic nontarget species is similar. The pyrethroids have different recommended field rates of application that are related to their efficacy, and the relationship between field rate and 10th centiles showed a trend. These results support the use of cypermethrin as a reasonable worst-case surrogate for the other pyrethroids for the purposes of risk assessment of pyrethroids as a class.

The National State Policy Database. Quick Turn Around (QTA).

ERIC Educational Resources Information Center

Ahearn, Eileen; Jackson, Terry

This paper describes the National State Policy Database (NSPD), a full-text searchable database of state and federal education regulations for special education. It summarizes the history of the NSPD and reports on a survey of state directors or their designees as to their use of the database and their suggestions for its future expansion. The…

76 FR 10405 - Federal Copyright Protection of Sound Recordings Fixed Before February 15, 1972

Federal Register 2010, 2011, 2012, 2013, 2014

2011-02-24

... file in either the Adobe Portable Document File (PDF) format that contains searchable, accessible text (not an image); Microsoft Word; WordPerfect; Rich Text Format (RTF); or ASCII text file format (not a..., comments may be delivered in hard copy. If hand delivered by a private party, an original [[Page 10406...

Ask an Anatomist: Identifying Global Trends, Topics and Themes of Academic Anatomists Using Twitter

ERIC Educational Resources Information Center

Marsland, Madeleine J.; Lazarus, Michelle D.

2018-01-01

Social media (SoMe) is increasingly used in higher education (HE) to access knowledge and enable global communication. The SoMe platform Twitter® is particularly beneficial in these contexts because it is readily accessible, easily searchable (via hashtags) and global. Given these advantages, the twitter platform @AskAnatomist was created to…

75 FR 14401 - Amendment of Certain of the Commission's Rules of Practice and Procedure and Rules of Commission...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-03-25

... were created, such as Microsoft Excel, Microsoft Word, or Microsoft PowerPoint (``native format'')? We... (condensed) or expanded (detailed) format Export search results to Excel or PDF As noted above, system is...., Microsoft Word ``.doc'' format or non-copy protected text- searchable ``.pdf'' format)? Should submissions...

Same City, New Scene: 2010 BEA Preview

ERIC Educational Resources Information Center

Katterjohn, Anna

2010-01-01

On May 25-26 in New York, BookExpo America (BEA) will present new events for participants. To lighten participants' totes, BEA is partnering with Above the Treeline to create a free online catalog (Books@BEA) of the new and forthcoming titles on the show floor. There will also be a searchable database of all the authors participating in show…

Whole genome sequences of the USMARC sheep diversity panel v 2.4 aligned to the ovine reference genome assembly

USDA-ARS?s Scientific Manuscript database

A searchable and publicly viewable set of mapped genomes from 96 rams from 9 US sheep breeds was created. The nine pure breeds were selected to represent genetic diversity for traits such as fertility, prolificacy, maternal ability, growth rate, carcass leanness, wool quality, mature weight, and lo...

Home Page: NYS Government Information Locator Service: New York State

Science.gov Websites

Constitution external link - from the New York State Department of State NYS Judicial System (NYS Unified Courts System) Unified Court System external link - the main resource for information about New York's decisions of the New York courts in the Official Reports. The searchable Legal Research Portal external link

Accessing a personalized bibliography with a searchable system on the World Wide Web

Treesearch

Malchus B. Baker; Daniel P. Huebner; Peter F. Ffolliott

2000-01-01

Researchers, educator's and land management personnel routinely construct bibliographies to assist them in managing publications that relate to their work. These personalized bibliographies are unique and valuable to others in the same discipline. This paper presents a computer data base system that provides users with the ability to search a bibliography through...

arXiv.org and Physics Education

ERIC Educational Resources Information Center

Ramlo, Susan

2007-01-01

The website arXiv.org (pronounced "archive") is a free online resource for full-text articles in the fields of physics, mathematics, computer science, nonlinear science, and quantitative biology that has existed for about 15 years. Available directly at http://www.arXiv.org, this e-print archive is searchable. As of Jan. 3, 2007, arXiv had open…

A searchable, whole genome resource designed for protein variant analysis in diverse lineages of U.S. beef cattle

USDA-ARS?s Scientific Manuscript database

A key feature of a gene's function is the variety of protein isoforms it encodes in a population. However, the genetic diversity in bovine whole genome databases tends to be underrepresented because these databases contain an abundance of sequence from the most influential sires. Our first aim was ...

Computers Track the Elusive Metaphor

ERIC Educational Resources Information Center

Guernsey, Lisa

2009-01-01

Computers may not be able to master poetics like Aristotle, but they have become smart enough to know a metaphor when they see one. An online database called The Mind Is a Metaphor, created by Brad Pasanek, an assistant professor of English at the University of Virginia, is a searchable bank of phrases, verses, and lines from literature that…

Yahoo Works with Academic Libraries on a New Project to Digitize Books

ERIC Educational Resources Information Center

Carlson, Scott; Young, Jeffrey R.

2005-01-01

This article reports on the most recent search-engine company to join with academic libraries in digitizing large collections of books to make them easily searchable online. Yahoo Inc. has teamed up with the University of California system, the University of Toronto, and several archives and technology companies on a project that could potentially…

The North Carolina State University Libraries Search Experience: Usability Testing Tabbed Search Interfaces for Academic Libraries

ERIC Educational Resources Information Center

Teague-Rector, Susan; Ballard, Angela; Pauley, Susan K.

2011-01-01

Creating a learnable, effective, and user-friendly library Web site hinges on providing easy access to search. Designing a search interface for academic libraries can be particularly challenging given the complexity and range of searchable library collections, such as bibliographic databases, electronic journals, and article search silos. Library…

Places to Go: Google's Search Results for "Net Generation"

ERIC Educational Resources Information Center

Downes, Stephen

2007-01-01

In his Places to Go column for a special issue on the Net Generation, Stephen Downes takes an unexpected trip--to Google. According to Downes, Google epitomizes the essence of the Net Generation. Infinitely searchable and adaptable, Google represents the spirit of a generation raised in the world of the Internet, a generation that adapts…

10 CFR 2.1013 - Use of the electronic docket during the proceeding.

Code of Federal Regulations, 2012 CFR

2012-01-01

... searchable full text, by header and image, as appropriate. (b) Absent good cause, all exhibits tendered... circumstances where submitters may need to use an image scanned before January 1, 2004, in a document created after January 1, 2004, or the scanning process for a large, one-page image may not successfully complete...

The Technology Education Graduate Research Database, 1892-2000. CTTE Monograph.

ERIC Educational Resources Information Center

Reed, Philip A., Ed.

The Technology Education Graduate Research Database (TEGRD) was designed in two parts. The first part was a 384 page bibliography of theses and dissertations from 1892-2000. The second part was an online, searchable database of graduate research completed within technology education from 1892 to the present. The primary goals of the project were:…

Key findings on legal and regulatory barriers to HIV testing and access to care across Europe.

PubMed

Power, L; Hows, J; Jakobsen, S F

2018-02-01

The aim of this work within OptTEST by HiE has been to demonstrate the role of legal and regulatory barriers in hindering access to HIV testing, treatment and care across Europe and to produce tools to help dismantle them. An online survey to assess country-specific data on legal and regulatory barriers distributed widely across the WHO Europe region. Literature reviews conducted in January-October 2015 in English, in November 2015 in Russian, and updated in April 2017. Semi-structured interviews were conducted with 25 key actors within the HIV field to feed into case studies and tip sheets on how to dismantle legal and regulatory barriers. More than 160 individuals and organisations from 49 countries across the WHO European region provided responses which were analysed and cross checked with other data sources and a searchable database produced (legalbarriers.peoplewithhiveurope.org). The conducted literature reviews yielded 88 papers and reports which identify legal and regulatory barriers to key populations' access to HV testing and care. Based on the interviews with key actors, ranging from PLHIV activists to government officials, on lessons-learned, a series of tip sheets and ten case studies were written-up intended to inform and inspire the HIV community to address and overcome existing barriers (opttest.eu/Tools). While some of the barriers identified may require major changes to wider health systems, or long term legal reform, many are open to a simple change in regulations or custom and practice. We have the tools. Why can't we finish the job? © 2018 British HIV Association.

Offshore Installations and Their Relevance to the Coast Guard through the Next Twenty-Five Years. Volume I. Basic Report: Forecast of Offshore Installations and Their Implications to the Coast Guard.

DTIC Science & Technology

1980-11-01

institution to impose charges on members of the Coast Guard’s constituency who benefit from Coast Guard sevices --i.e. establish user charges and value... Sex Ratio - Externalities * Labor Force - Relation to economic growth - Nature and number - Man’s welfare - Participation rate - Productivity rate...Pollution characterisitcs - Sex distribution Radioactive e By Country Thermal Toxic 9 Structure Contanimant - Stratification Long run/short run

PROPOSED STANDARD TO GREATLY EXPAND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT

EPA Science Inventory

PROPOSED ST ANDARD TO GREA TL Y EXP AND PUBLIC ACCESS AND EXPLORATION OF TOXICITY DATA: EVALUATION OF STRUCTURE DATA FILE FORMAT

The ability to assess the potential toxicity of environmental, pharmaceutical, or industrial chemicals based on chemical structure in...

Modifications to toxic CUG RNAs induce structural stability, rescue mis-splicing in a myotonic dystrophy cell model and reduce toxicity in a myotonic dystrophy zebrafish model

DOE PAGES

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy; ...

2014-10-10

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

Analysis of sublethal arsenic toxicity to Ceratophyllum demersum: subcellular distribution of arsenic and inhibition of chlorophyll biosynthesis.

PubMed

Mishra, Seema; Alfeld, Matthias; Sobotka, Roman; Andresen, Elisa; Falkenberg, Gerald; Küpper, Hendrik

2016-08-01

Arsenic (As) pollution is a serious concern worldwide. Recent studies under environmentally relevant conditions revealed that, in the aquatic plant Ceratophyllum demersum, pigments are the first observable target of toxicity, prior to any effect on photosynthetic parameters or to oxidative stress. Lethal toxicity was initiated by a change of As species and their distribution pattern in various tissues. Here, the localization of As was investigated at the subcellular level through X-ray fluorescence using a submicron beam and a Maia detector. Further, it was possible to obtain useful tissue structural information from the ratio of the tomogram of photon flux behind the sample to the tomogram of Compton scattering. The micro-X-ray fluorescence tomograms showed that As predominantly accumulated in the nucleus of the epidermal cells in young mature leaves exposed to sublethal 1 µM As. This suggests that As may exert toxic effects in the nucleus, for example, by interfering with nucleic acid synthesis by replacing phosphorous with As. At higher cellular concentrations, As was mainly stored in the vacuole, particularly in mature leaves. An analysis of precursors of chlorophyll and degradation metabolites revealed that the observed decrease in chlorophyll concentration was associated with hindered biosynthesis, and was not due to degradation. Coproporphyrinogen III could not be detected after exposure to only 0.5 µM As. Levels of subsequent precursors, for example, protoporphyrin IX, Mg-protoporphyrin, Mg-protoporphyrin methyl ester, and divinyl protochlorophyllide, were significantly decreased at this concentration as well, indicating that the pathway was blocked upstream of tetrapyrrole synthesis. © The Author 2016. Published by Oxford University Press on behalf of the Society for Experimental Biology.

Accumulation and distribution of Zn in the shoots and reproductive structures of the halophyte plant species Kosteletzkya virginica as a function of salinity.

PubMed

Han, Ruiming; Quinet, Muriel; André, Emilie; van Elteren, Johannes Teun; Destrebecq, Florence; Vogel-Mikuš, Katarina; Cui, Guangling; Debeljak, Marta; Lefèvre, Isabelle; Lutts, Stanley

2013-09-01

Kosteletzkya virginica is a wetland halophyte that is a good candidate for rehabilitation of degraded salt marshes and production of oil as biodiesel. Salt marshes are frequently contaminated by heavy metals. The distribution of Zn in vegetative and reproductive organs of adult plants, and the NaCl influence on this distribution remain unknown and were thus explored in the present study. Plants were cultivated in a nutrient film technique system, from seedling stage until seed maturation in a control, Zn (100 μM), NaCl (50 mM) or Zn + NaCl medium. Photosynthesis, ion nutrition, malondialdehyde and non-protein thiol concentrations were quantified. Zinc distribution in reproductive organs was estimated by a laser ablation-inductively coupled plasma-mass spectrometry procedure (LA-ICP-MS). Adult plants accumulated up to 2 mg g(-1) DW Zn in the shoots. Zinc reduced plant growth, inhibited photosynthesis and reduced seed yield. Zinc accumulation in the seeds was only two times higher in Zn-treated plants than in controls. Exogenous NaCl neutralized the damaging action of Zn and modified the Zn distribution through a preferential accumulation of toxic ions in older leaves. Zinc was present in seed testa, endosperm and, to a lower extent, in embryo. Additional NaCl induced a chalazal retention of Zn during seed maturation and reduced final Zn seed content. It is concluded that NaCl 50 mM had a positive impact on the response of K. virginica to Zn toxicity and acts through a modification in Zn distribution rather than a decrease in Zn absorption.

Convection-enhanced drug delivery of interleukin-4 Pseudomonas exotoxin (PRX321): increased distribution and magnetic resonance monitoring.

PubMed

Mardor, Y; Last, D; Daniels, D; Shneor, R; Maier, S E; Nass, D; Ram, Z

2009-08-01

Convection-enhanced drug delivery (CED) enables achieving a drug concentration within brain tissue and brain tumors that is orders of magnitude higher than by systemic administration. Previous phase I/II clinical trials using intratumoral convection of interleukin-4 Pseudomonas exotoxin (PRX321) have demonstrated an acceptable safety and toxicity profile with promising signs of therapeutic activity. The present study was designed to assess the distribution efficiency and toxicity of this PRX321 using magnetic resonance imaging (MRI) and to test whether reformulation with increased viscosity could enhance drug distribution. Convection of low- [0.02% human serum albumin (HSA)] and high-viscosity (3% HSA) infusates mixed with gadolinium-diethylenetriamine pentaacetic acid and PRX321 were compared with low- and high-viscosity infusates without the drug, in normal rat brains. MRI was used for assessment of drug distribution and detection of early and late toxicity. Representative brain samples were subjected to histological examination. Distribution volumes calculated from the magnetic resonance images showed that the average distribution of 0.02% HSA was larger than that of 0.02% HSA with PRX321 by a factor of 1.98 (p < 0.02). CED of 3.0% HSA, with or without PRX321, tripled the volume of distribution compared with 0.02% HSA with PRX321 (p < 0.015). No drug-related toxicity was detected. These results suggest that the impeded convection of the PRX321 infusate used in previous clinical trials can be reversed by increasing infusate viscosity and lead to tripling of the volume of distribution. This effect was not associated with any detectable toxicity. A similar capability to reverse impeded convection was also demonstrated in a CED model using acetic acid. These results will be implemented in an upcoming phase IIb PRX321 CED trial with a high-viscosity infusate.

Cobalt distribution in keratinocyte cells indicates nuclear and perinuclear accumulation and interaction with magnesium and zinc homeostasis.

PubMed

Ortega, Richard; Bresson, Carole; Fraysse, Aurélien; Sandre, Caroline; Devès, Guillaume; Gombert, Clémentine; Tabarant, Michel; Bleuet, Pierre; Seznec, Hervé; Simionovici, Alexandre; Moretto, Philippe; Moulin, Christophe

2009-07-10

Cobalt is known to be toxic at high concentration, to induce contact dermatosis, and occupational radiation skin damage because of its use in nuclear industry. We investigated the intracellular distribution of cobalt in HaCaT human keratinocytes as a model of skin cells, and its interaction with endogenous trace elements. Direct micro-chemical imaging based on ion beam techniques was applied to determine the quantitative distribution of cobalt in HaCaT cells. In addition, synchrotron radiation X-ray fluorescence microanalysis in tomography mode was performed, for the first time on a single cell, to determine the 3D intracellular distribution of cobalt. Results obtained with these micro-chemical techniques were compared to a more classical method based on cellular fractionation followed by inductively coupled plasma atomic emission spectrometry (ICP-AES) measurements. Cobalt was found to accumulate in the cell nucleus and in perinuclear structures indicating the possible direct interaction with genomic DNA, and nuclear proteins. The perinuclear accumulation in the cytosol suggests that cobalt could be stored in the endoplasmic reticulum or the Golgi apparatus. The multi-elemental analysis revealed that cobalt exposure significantly decreased magnesium and zinc content, with a likely competition of cobalt for magnesium and zinc binding sites in proteins. Overall, these data suggest a multiform toxicity of cobalt related to interactions with genomic DNA and nuclear proteins, and to the alteration of zinc and magnesium homeostasis.

The Planetary Data System— Archiving Planetary Data for the use of the Planetary Science Community

NASA Astrophysics Data System (ADS)

Morgan, Thomas H.; McLaughlin, Stephanie A.; Grayzeck, Edwin J.; Vilas, Faith; Knopf, William P.; Crichton, Daniel J.

2014-11-01

NASA’s Planetary Data System (PDS) archives, curates, and distributes digital data from NASA’s planetary missions. PDS provides the planetary science community convenient online access to data from NASA’s missions so that they can continue to mine these rich data sets for new discoveries. The PDS is a federated system consisting of nodes for specific discipline areas ranging from planetary geology to space physics. Our federation includes an engineering node that provides systems engineering support to the entire PDS.In order to adequately capture complete mission data sets containing not only raw and reduced instrument data, but also calibration and documentation and geometry data required to interpret and use these data sets both singly and together (data from multiple instruments, or from multiple missions), PDS personnel work with NASA missions from the initial AO through the end of mission to define, organize, and document the data. This process includes peer-review of data sets by members of the science community to ensure that the data sets are scientifically useful, effectively organized, and well documented. PDS makes the data in PDS easily searchable so that members of the planetary community can both query the archive to find data relevant to specific scientific investigations and easily retrieve the data for analysis. To ensure long-term preservation of data and to make data sets more easily searchable with the new capabilities in Information Technology now available (and as existing technologies become obsolete), the PDS (together with the COSPAR sponsored IPDA) developed and deployed a new data archiving system known as PDS4, released in 2013. The LADEE, MAVEN, OSIRIS REx, InSight, and Mars2020 missions are using PDS4. ESA has adopted PDS4 for the upcoming BepiColumbo mission. The PDS is actively migrating existing data records into PDS4 and developing tools to aid data providers and users. The PDS is also incorporating challenge-based competitions to rapidly and economically develop new tools for both users and data providers.Please visit our User Support Area at the meeting (Booth #114) if you have questions accessing our data sets or providing data to the PDS.

Current Development at the Southern California Earthquake Data Center (SCEDC)

NASA Astrophysics Data System (ADS)

Appel, V. L.; Clayton, R. W.

2005-12-01

Over the past year, the SCEDC completed or is near completion of three featured projects: Station Information System (SIS) Development: The SIS will provide users with an interface into complete and accurate station metadata for all current and historic data at the SCEDC. The goal of this project is to develop a system that can interact with a single database source to enter, update and retrieve station metadata easily and efficiently. The system will provide accurate station/channel information for active stations to the SCSN real-time processing system, as will as station/channel information for stations that have parametric data at the SCEDC i.e., for users retrieving data via STP. Additionally, the SIS will supply information required to generate dataless SEED and COSMOS V0 volumes and allow stations to be added to the system with a minimum, but incomplete set of information using predefined defaults that can be easily updated as more information becomes available. Finally, the system will facilitate statewide metadata exchange for both real-time processing and provide a common approach to CISN historic station metadata. Moment Tensor Solutions: The SCEDC is currently archiving and delivering Moment Magnitudes and Moment Tensor Solutions (MTS) produced by the SCSN in real-time and post-processing solutions for events spanning back to 1999. The automatic MTS runs on all local events with magnitudes > 3.0, and all regional events > 3.5. The distributed solution automatically creates links from all USGS Simpson Maps to a text e-mail summary solution, creates a .gif image of the solution, and updates the moment tensor database tables at the SCEDC. Searchable Scanned Waveforms Site: The Caltech Seismological Lab has made available 12,223 scanned images of pre-digital analog recordings of major earthquakes recorded in Southern California between 1962 and 1992 at http://www.data.scec.org/research/scans/. The SCEDC has developed a searchable web interface that allows users to search the available files, select multiple files for download and then retrieve a zipped file containing the results. Scanned images of paper records for M>3.5 southern California earthquakes and several significant teleseisms are available for download via the SCEDC through this search tool.

Toxic Warfare

DTIC Science & Technology

2002-02-01

Prepared for the United States Air Force Approved for public release; distribution unlimited Theodore Karasik Project AIR FORCE R TOXIC WARFARE...Report Documentation Page Report Date 000002002 Report Type N/A Dates Covered (from... to) - Title and Subtitle Toxic Warfare Contract Number Grant...310) 451-6915; Email: order@rand.org Library of Congress Cataloging-in-Publication Data Karasik, Theodore William. Toxic warfare / Theodore Karasik

MytiBase: a knowledgebase of mussel (M. galloprovincialis) transcribed sequences

PubMed Central

Venier, Paola; De Pittà, Cristiano; Bernante, Filippo; Varotto, Laura; De Nardi, Barbara; Bovo, Giuseppe; Roch, Philippe; Novoa, Beatriz; Figueras, Antonio; Pallavicini, Alberto; Lanfranchi, Gerolamo

2009-01-01

Background Although Bivalves are among the most studied marine organisms due to their ecological role, economic importance and use in pollution biomonitoring, very little information is available on the genome sequences of mussels. This study reports the functional analysis of a large-scale Expressed Sequence Tag (EST) sequencing from different tissues of Mytilus galloprovincialis (the Mediterranean mussel) challenged with toxic pollutants, temperature and potentially pathogenic bacteria. Results We have constructed and sequenced seventeen cDNA libraries from different Mediterranean mussel tissues: gills, digestive gland, foot, anterior and posterior adductor muscle, mantle and haemocytes. A total of 24,939 clones were sequenced from these libraries generating 18,788 high-quality ESTs which were assembled into 2,446 overlapping clusters and 4,666 singletons resulting in a total of 7,112 non-redundant sequences. In particular, a high-quality normalized cDNA library (Nor01) was constructed as determined by the high rate of gene discovery (65.6%). Bioinformatic screening of the non-redundant M. galloprovincialis sequences identified 159 microsatellite-containing ESTs. Clusters, consensuses, related similarities and gene ontology searches have been organized in a dedicated, searchable database . Conclusion We defined the first species-specific catalogue of M. galloprovincialis ESTs including 7,112 unique transcribed sequences. Putative microsatellite markers were identified. This annotated catalogue represents a valuable platform for expression studies, marker validation and genetic linkage analysis for investigations in the biology of Mediterranean mussels. PMID:19203376

Evaluating the Spatial Distribution of Toxic Air Contaminants in Multiple Ecosystem Indicators in the Sierra Nevada-Southern Cascades

NASA Astrophysics Data System (ADS)

Nanus, L.; Simonich, S. L.; Rocchio, J.; Flanagan, C.

2013-12-01

Toxic air contaminants originating from agricultural areas of the Central Valley in California threaten vulnerable sensitive receptors including surface water, vegetation, snow, sediments, fish, and amphibians in the Sierra Nevada-Southern Cascades region. The spatial distribution of toxic air contaminants in different ecosystem indicators depends on variation in atmospheric concentrations and deposition, and variation in air toxics accumulation in ecosystems. The spatial distribution of organic air toxics and mercury at over 330 unique sampling locations and sample types over two decades (1990-2009) in the Sierra Nevada-Southern Cascades region were compiled and maps were developed to further understand spatial patterns and linkages between air toxics deposition and ecological effects. Potential ecosystem impacts in the Sierra Nevada-Southern Cascades region include bioaccumulation of air toxics in both aquatic and terrestrial ecosystems, reproductive disruption, and immune suppression. The most sensitive ecological end points in the region that are affected by bioaccumulation of toxic air contaminants are fish. Mercury was detected in all fish and approximately 6% exceeded human consumption thresholds. Organic air toxics were also detected in fish yielding variable spatial patterns. For amphibians, which are sensitive to pesticide exposure and potential immune suppression, increasing trends in current and historic use pesticides are observed from north to south across the region. In other indicators, such as vegetation, pesticide concentrations in lichen increase with increasing elevation. Current and historic use pesticides and mercury were also observed in snowpack at high elevations in the study area. This study shows spatial patterns in toxic air contaminants, evaluates associated risks to sensitive receptors, and identifies data gaps. Future research on atmospheric modeling and information on sources is needed in order to predict which ecosystems are the most sensitive to toxic air contaminants in the Sierra Nevada-Southern Cascades region.

Distributed data discovery, access and visualization services to Improve Data Interoperability across different data holdings

NASA Astrophysics Data System (ADS)

Palanisamy, G.; Krassovski, M.; Devarakonda, R.; Santhana Vannan, S.

2012-12-01

The current climate debate is highlighting the importance of free, open, and authoritative sources of high quality climate data that are available for peer review and for collaborative purposes. It is increasingly important to allow various organizations around the world to share climate data in an open manner, and to enable them to perform dynamic processing of climate data. This advanced access to data can be enabled via Web-based services, using common "community agreed" standards without having to change their internal structure used to describe the data. The modern scientific community has become diverse and increasingly complex in nature. To meet the demands of such diverse user community, the modern data supplier has to provide data and other related information through searchable, data and process oriented tool. This can be accomplished by setting up on-line, Web-based system with a relational database as a back end. The following common features of the web data access/search systems will be outlined in the proposed presentation: - A flexible data discovery - Data in commonly used format (e.g., CSV, NetCDF) - Preparing metadata in standard formats (FGDC, ISO19115, EML, DIF etc.) - Data subseting capabilities and ability to narrow down to individual data elements - Standards based data access protocols and mechanisms (SOAP, REST, OpenDAP, OGC etc.) - Integration of services across different data systems (discovery to access, visualizations and subseting) This presentation will also include specific examples of integration of various data systems that are developed by Oak Ridge National Laboratory's - Climate Change Science Institute, their ability to communicate between each other to enable better data interoperability and data integration. References: [1] Devarakonda, Ranjeet, and Harold Shanafield. "Drupal: Collaborative framework for science research." Collaboration Technologies and Systems (CTS), 2011 International Conference on. IEEE, 2011. [2]Devarakonda, R., Shrestha, B., Palanisamy, G., Hook, L. A., Killeffer, T. S., Boden, T. A., ... & Lazer, K. (2014). THE NEW ONLINE METADATA EDITOR FOR GENERATING STRUCTURED METADATA. Oak Ridge National Laboratory (ORNL).

Music to Our Eyes: Google Books, Google Scholar, and the Open Content Alliance

ERIC Educational Resources Information Center

Dougan, Kirstin

2010-01-01

The Internet has changed how scholars perform their research. With more and more content available online that is fully searchable (often even for free), it is not surprising that students and others may turn there first before coming to the library. This study aims to identify the utility of three of the largest free access points to print…

Refining the Use of the Web (and Web Search) as a Language Teaching and Learning Resource

ERIC Educational Resources Information Center

Wu, Shaoqun; Franken, Margaret; Witten, Ian H.

2009-01-01

The web is a potentially useful corpus for language study because it provides examples of language that are contextualized and authentic, and is large and easily searchable. However, web contents are heterogeneous in the extreme, uncontrolled and hence "dirty," and exhibit features different from the written and spoken texts in other linguistic…

How To Do Field Searching in Web Search Engines: A Field Trip.

ERIC Educational Resources Information Center

Hock, Ran

1998-01-01

Describes the field search capabilities of selected Web search engines (AltaVista, HotBot, Infoseek, Lycos, Yahoo!) and includes a chart outlining what fields (date, title, URL, images, audio, video, links, page depth) are searchable, where to go on the page to search them, the syntax required (if any), and how field search queries are entered.…

4Kids.org: Topical, Searchable, and Safe Internet-Based Resource for Children and Youth

ERIC Educational Resources Information Center

Bacon, Melanie; Blood, Leslie; Ault, Marilyn; Adams, Doug

2008-01-01

4Kids.org is an online resource with an accompanying syndicated print publication created to promote safe access to websites and technology literacy. 4Kids.org, created by ALTEC at the University of Kansas in 1995, provides a variety of Internet-based activities as well as access to a database of websites reviewed for educational content,…

Workforce Modeling & Simulation Education and Training for Lifelong Learning: Modeling & Simulation Education Catalog

DTIC Science & Technology

2007-03-01

LEARNING : MODELING & SIMULATION EDUCATION CATALOG by Jean Catalano Jarema M. Didoszak March 2007...Technical Report, 11/06 – 02/07 4. TITLE AND SUBTITLE: Workforce Modeling & Simulation Education and Training for Lifelong Learning ...Modeling and Simulation Education and Training for Lifelong Learning project. The catalog contains searchable information about 253 courses from 23 U.S

An Analysis of Implementation Issues for the Searchable Content Object Reference Model (SCORM) in Navy Education and Training

DTIC Science & Technology

2003-09-01

content objects to be used and reused within civilian and military education and training Learning Management Systems (LMS) across the World Wide Web...to be used and reused within civilian and military education and training Learning Management Systems (LMS) across the World Wide Web. vi...1998, SUBJECT: ENHANCING LEARNING AND EDUCATION THROUGH TECHNOLOGY

Online Resources for Identifying Evidence-Based, Out-of-School Time Programs: A User's Guide. Research-to-Results Brief. Publication #2009-36

ERIC Educational Resources Information Center

Terzian; Mary; Moore, Kristin Anderson; Williams-Taylor, Lisa; Nguyen, Hoan

2009-01-01

Child Trends produced this Guide to assist funders, administrators, and practitioners in identifying and navigating online resources to find evidence-based programs that may be appropriate for their target populations and communities. The Guide offers an overview of 21 of these resources--11 searchable online databases, 2 online interactive…

Nuclear data made easily accessible through the Notre Dame Nuclear Database

NASA Astrophysics Data System (ADS)

Khouw, Timothy; Lee, Kevin; Fasano, Patrick; Mumpower, Matthew; Aprahamian, Ani

2014-09-01

In 1994, the NNDC revolutionized nuclear research by providing a colorful, clickable, searchable database over the internet. Over the last twenty years, web technology has evolved dramatically. Our project, the Notre Dame Nuclear Database, aims to provide a more comprehensive and broadly searchable interactive body of data. The database can be searched by an array of filters which includes metadata such as the facility where a measurement is made, the author(s), or date of publication for the datum of interest. The user interface takes full advantage of HTML, a web markup language, CSS (cascading style sheets to define the aesthetics of the website), and JavaScript, a language that can process complex data. A command-line interface is supported that interacts with the database directly on a user's local machine which provides single command access to data. This is possible through the use of a standardized API (application programming interface) that relies upon well-defined filtering variables to produce customized search results. We offer an innovative chart of nuclides utilizing scalable vector graphics (SVG) to deliver users an unsurpassed level of interactivity supported on all computers and mobile devices. We will present a functional demo of our database at the conference.

Implementation and application of an interactive user-friendly validation software for RADIANCE

NASA Astrophysics Data System (ADS)

Sundaram, Anand; Boonn, William W.; Kim, Woojin; Cook, Tessa S.

2012-02-01

RADIANCE extracts CT dose parameters from dose sheets using optical character recognition and stores the data in a relational database. To facilitate validation of RADIANCE's performance, a simple user interface was initially implemented and about 300 records were evaluated. Here, we extend this interface to achieve a wider variety of functions and perform a larger-scale validation. The validator uses some data from the RADIANCE database to prepopulate quality-testing fields, such as correspondence between calculated and reported total dose-length product. The interface also displays relevant parameters from the DICOM headers. A total of 5,098 dose sheets were used to test the performance accuracy of RADIANCE in dose data extraction. Several search criteria were implemented. All records were searchable by accession number, study date, or dose parameters beyond chosen thresholds. Validated records were searchable according to additional criteria from validation inputs. An error rate of 0.303% was demonstrated in the validation. Dose monitoring is increasingly important and RADIANCE provides an open-source solution with a high level of accuracy. The RADIANCE validator has been updated to enable users to test the integrity of their installation and verify that their dose monitoring is accurate and effective.

An automated, web-enabled and searchable database system for archiving electrogram and related data from implantable cardioverter defibrillators.

PubMed

Zong, W; Wang, P; Leung, B; Moody, G B; Mark, R G

2002-01-01

The advent of implantable cardioverter defibrillators (ICDs) has resulted in significant reductions in mortality in patients at high risk for sudden cardiac death. Extensive related basic research and clinical investigation continue. ICDs typically record intracardiac electrograms and inter-beat intervals along with device settings during episodes of device delivery of therapy. Researchers wishing to study these data further have until now been limited to viewing paper plots. In support of multi-center clinical studies of patients with ICDs, we have developed a web based searchable ICD data archiving system, which allows users to use a web browser to upload ICD data from diskettes to a server where the data are automatically processed and archived. Users can view and download the archived ICD data directly via the web. The entire system is built from open source software. At present more than 500 patient ICD data sets have been uploaded to and archived in the system. This project will be of value not only to those who wish to conduct research using ICD data, but also to clinicians who need to archive and review ICD data collected from their patients.

The CTSA Consortium's Catalog of Assets for Translational and Clinical Health Research (CATCHR)

PubMed Central

Mapes, Brandy; Basford, Melissa; Zufelt, Anneliese; Wehbe, Firas; Harris, Paul; Alcorn, Michael; Allen, David; Arnim, Margaret; Autry, Susan; Briggs, Michael S.; Carnegie, Andrea; Chavis‐Keeling, Deborah; De La Pena, Carlos; Dworschak, Doris; Earnest, Julie; Grieb, Terri; Guess, Marilyn; Hafer, Nathaniel; Johnson, Tesheia; Kasper, Amanda; Kopp, Janice; Lockie, Timothy; Lombardo, Vincetta; McHale, Leslie; Minogue, Andrea; Nunnally, Beth; O'Quinn, Deanna; Peck, Kelly; Pemberton, Kieran; Perry, Cheryl; Petrie, Ginny; Pontello, Andria; Posner, Rachel; Rehman, Bushra; Roth, Deborah; Sacksteder, Paulette; Scahill, Samantha; Schieri, Lorri; Simpson, Rosemary; Skinner, Anne; Toussant, Kim; Turner, Alicia; Van der Put, Elaine; Wasser, June; Webb, Chris D.; Williams, Maija; Wiseman, Lori; Yasko, Laurel; Pulley, Jill

2014-01-01

Abstract The 61 CTSA Consortium sites are home to valuable programs and infrastructure supporting translational science and all are charged with ensuring that such investments translate quickly to improved clinical care. Catalog of Assets for Translational and Clinical Health Research (CATCHR) is the Consortium's effort to collect and make available information on programs and resources to maximize efficiency and facilitate collaborations. By capturing information on a broad range of assets supporting the entire clinical and translational research spectrum, CATCHR aims to provide the necessary infrastructure and processes to establish and maintain an open‐access, searchable database of consortium resources to support multisite clinical and translational research studies. Data are collected using rigorous, defined methods, with the resulting information made visible through an integrated, searchable Web‐based tool. Additional easy‐to‐use Web tools assist resource owners in validating and updating resource information over time. In this paper, we discuss the design and scope of the project, data collection methods, current results, and future plans for development and sustainability. With increasing pressure on research programs to avoid redundancy, CATCHR aims to make available information on programs and core facilities to maximize efficient use of resources. PMID:24456567

Quantitative structure-toxicity relationship (QSTR) studies on the organophosphate insecticides.

PubMed

Can, Alper

2014-11-04

Organophosphate insecticides are the most commonly used pesticides in the world. In this study, quantitative structure-toxicity relationship (QSTR) models were derived for estimating the acute oral toxicity of organophosphate insecticides to male rats. The 20 chemicals of the training set and the seven compounds of the external testing set were described by means of using descriptors. Descriptors for lipophilicity, polarity and molecular geometry, as well as quantum chemical descriptors for energy were calculated. Model development to predict toxicity of organophosphate insecticides in different matrices was carried out using multiple linear regression. The model was validated internally and externally. In the present study, QSTR model was used for the first time to understand the inherent relationships between the organophosphate insecticide molecules and their toxicity behavior. Such studies provide mechanistic insight about structure-toxicity relationship and help in the design of less toxic insecticides. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Mercury toxicity to freshwater organisms: extrapolation using species sensitivity distribution.

PubMed

Rodrigues, Andreia C M; Jesus, Fátima T; Fernandes, Marco A F; Morgado, Fernando; Soares, Amadeu M V M; Abreu, Sizenando N

2013-08-01

Mercury toxicity to aquatic organisms was evaluated in different taxonomic groups showing the following species sensitivity gradient: Daphnia magna > Daphnia longispina > Pseudokirchneriella subcapitata > Chlorella vulgaris > Lemna minor > Chironomus riparius. Toxicity values ranged from 3.49 μg/L (48 h-EC₅₀ of D. magna) to 1.58 mg/L (48 h-EC₅₀ of C. riparius). A species sensitivity distribution was used to estimate hazardous mercury concentration at 5 % level (HC5) and the predicted no effect concentration (PNEC). The HC5 was 3.18 μg Hg/L and the PNEC varied between 0.636 and 3.18 μg Hg/L, suggesting no risk of acute toxicity to algae, plants, crustaceans and insects in most freshwaters.

Quantitative Structure-Activity Relationships for Organophosphate Enzyme Inhibition (Briefing Charts)

DTIC Science & Technology

2011-09-22

OPs) are a group of pesticides that inhibit enzymes such as acetylcholinesterase. Numerous OP structural variants exist and toxicity data can be...and human toxicity studies especially for OPs lacking experimental data. 15. SUBJECT TERMS QSAR Organophosphates...structure and mechanism of toxicity c) Linking QSAR and OP PBPK/PD 2. Methods a) Physiochemical Descriptors b) Regression Techniques 3. Results a

Evaluation of In Silico Anti-parkinson potential of β-asarone.

PubMed

Gupta, Meenakshi; Kant, Kamal; Sharma, Ruchika; Kumar, Anoop

2018-04-16

Parkinson's disease is affecting millions of people worldwide. The prevalence of Parkinson's disease is 0.3% globally, rising to 1% in more than 60 years of age and 4% in more than 80 years of age and the figures are thought to be doubled by 2030. Thus, there is a great need to identify novel therapeutic strategies or candidate drug molecule which can rescue neuronal degeneration. β-asarone has potential to act as a neuroprotective agent but regarding its role in Parkinson disease, very few reports are available. Thus, this study was undertaken to unlock the potential of β-asarone against Parkinson's disease. The Absorption, Distribution, Metabolism, and Excretion (ADME) analysis has been done by using Swiss ADME Predictor. The interactions of β-asarone towards dopaminergic receptors were investigated by Glide Program 5.0. The crystal structures of dopamine receptors were retrieved from Research Collaboratory for Structural Bioinformatics- Protein Data Bank (RCSB-PDB). The structure of β-asarone was drawn in Chem Draw Ultra 7.0.1. Finally, the toxicity of β-asarone has been predicted by using online web-servers like Lazar and Protox. The ADME data of current investigation has shown good oral bioavailability of β-asarone. It also showed a good binding affinity towards dopaminergic receptors. Further, it was found to be interacting through hydrogen bond with different amino acid residues of D2 and D3 receptors. However, β-asarone was predicted to be toxic in various species of rodents, as per the results of toxicity online web servers. Based on the current finding from ADME and docking studies, these preliminary results may act as effective precursor tool for development of β-asarone as a promising anti-Parkinson agent. However, furthermore experimental validation using in-vitro & in-vivo studies is needed to explore their therapeutic & toxic effects. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Importance of doping, dopant distribution, and defects on electronic band structure alteration of metal oxide nanoparticles: Implications for reactive oxygen species.

PubMed

Saleh, Navid B; Milliron, Delia J; Aich, Nirupam; Katz, Lynn E; Liljestrand, Howard M; Kirisits, Mary Jo

2016-10-15

Metal oxide nanoparticles (MONPs) are considered to have the potency to generate reactive oxygen species (ROS), one of the key mechanisms underlying nanotoxicity. However, the nanotoxicology literature demonstrates a lack of consensus on the dominant toxicity mechanism(s) for a particular MONP. Moreover, recent literature has studied the correlation between band structure of pristine MONPs to their ability to introduce ROS and thus has downplayed the ROS-mediated toxicological relevance of a number of such materials. On the other hand, material science can control the band structure of these materials to engineer their electronic and optical properties and thereby is constantly modulating the pristine electronic structure. Since band structure is the fundamental material property that controls ROS-producing ability, band tuning via introduction of dopants and defects needs careful consideration in toxicity assessments. This commentary critically evaluates the existing material science and nanotoxicity literature and identifies the gap in our understanding of the role of important crystal structure features (i.e., dopants and defects) on MONPs' electronic structure alteration as well as their ROS-generation capability. Furthermore, this commentary provides suggestions on characterization techniques to evaluate dopants and defects on the crystal structure and identifies research needs for advanced theoretical predictions of their electronic band structures and ROS-generation abilities. Correlation of electronic band structure and ROS will not only aid in better mechanistic assessment of nanotoxicity but will be impactful in designing and developing ROS-based applications ranging from water disinfection to next-generation antibiotics and even cancer therapeutics. Copyright © 2016 Elsevier B.V. All rights reserved.

Interspecies Correlation Estimation (ICE) models predict supplemental toxicity data for SSDs

EPA Science Inventory

Species sensitivity distributions (SSD) require a large number of toxicity values for a diversity of taxa to define a hazard level protective of multiple species. For most chemicals, measured toxicity data are limited to a few standard test species that are unlikely to adequately...

Enantiospecific toxicity, distribution and bioaccumulation of chiral antidepressant venlafaxine and its metabolite in loach (Misgurnus anguillicaudatus) co-exposed to microplastic and the drugs.

PubMed

Qu, Han; Ma, Ruixue; Wang, Bin; Yang, Jian; Duan, Lei; Yu, Gang

2018-04-22

In present study, we investigated the enantioselective behaviors of the chiral antidepressant venlafaxine and its metabolite O-desmethylvenlafaxine in loach Misgurnus anguillicaudatus (M. anguillicaudatus), as well as effects of microplastic on toxicity, distribution and metabolism through a 40-day co-exposure. The contents of SOD and MDA in loach liver elevated when the loach was exposed to venlafaxine and O-desmethylvenlafaxine. Moreover, co-exposure with microplastic might lead to more adverse effect against loach. The distribution of venlafaxine and O-desmethylvenlafaxine were both detected in loach tissues and liver subcellular. The concentrations of venlafaxine and O-desmethylvenlafaxine were lower in water in microplastic-present treatment. Whilst, more contaminants were accumulated in liver through the "vehicle" (microplastic). Enantioselective behavior of venlafaxine and O-desmethylvenlafaxine occurred with R-enantiomers being preferentially degraded. With microplastic present, the bioaccumulation factor (BAF) of venlafaxine and O-desmethylvenlafaxine in loach tissue amplified more than 10 times. In liver subcellular structure, microplastic may help to transport more compounds into subtle areas and postpone the contaminants metabolism in organisms. The present study for the first time gained an insight into the potential ecological effects and environmental behaviors of combined pollutions of chiral pharmaceuticals and microplastic, which could supply important information for environment risk assessment of concurrent organic pollutants and microplastic. Copyright © 2018 Elsevier B.V. All rights reserved.

Lupines, poison-hemlock and Nicotiana spp: toxicity and teratogenicity in livestock.

PubMed

Panter, K E; James, L F; Gardner, D R

1999-02-01

Many species of lupines contain quinolizidine or piperidine alkaloids known to be toxic or teratogenic to livestock. Poison-hemlock (Conium maculatum) and Nicotiana spp. including N. tabacum and N. glauca contain toxic and teratogenic piperidine alkaloids. The toxic and teratogenic effects from these plant species have distinct similarities including maternal muscular weakness and ataxia and fetal contracture-type skeletal defects and cleft palate. It is believed that the mechanism of action of the piperidine and quinolizidine alkaloid-induced teratogenesis is the same; however, there are some differences in incidence, susceptible gestational periods, and severity between livestock species. Wildlife species have also been poisoned after eating poison-hemlock but no terata have been reported. The most widespread problem for livestock producers in recent times has been lupine-induced "crooked calf disease." Crooked calf disease is characterized as skeletal contracture-type malformations and occasional cleft palate in calves after maternal ingestion of lupines containing the quinolizidine alkaloid anagyrine during gestation days 40-100. Similar malformations have been induced in cattle and goats with lupines containing the piperidine alkaloids ammodendrine, N-methyl ammodendrine, and N-acetyl hystrine and in cattle, sheep, goats, and pigs with poison-hemlock containing predominantly coniine or gamma-coniceine and N. glauca containing anabasine. Toxic and teratogenic effects have been linked to structural aspects of these alkaloids, and the mechanism of action is believed to be associated with an alkaloid-induced inhibition of fetal movement during specific gestational periods. This review presents a historical perspective, description and distribution of lupines, poison-hemlock and Nicotiana spp., toxic and teratogenic effects and management information to reduce losses.

Modeling corrosion inhibition efficacy of small organic molecules as non-toxic chromate alternatives using comparative molecular surface analysis (CoMSA).

PubMed

Fernandez, Michael; Breedon, Michael; Cole, Ivan S; Barnard, Amanda S

2016-10-01

Traditionally many structural alloys are protected by primer coatings loaded with corrosion inhibiting additives. Strontium Chromate (or other chromates) have been shown to be extremely effectively inhibitors, and find extensive use in protective primer formulations. Unfortunately, hexavalent chromium which imbues these coatings with their corrosion inhibiting properties is also highly toxic, and their use is being increasingly restricted by legislation. In this work we explore a novel tridimensional Quantitative-Structure Property Relationship (3D-QSPR) approach, comparative molecular surface analysis (CoMSA), which was developed to recognize "high-performing" corrosion inhibitor candidates from the distributions of electronegativity, polarizability and van der Waals volume on the molecular surfaces of 28 small organic molecules. Multivariate statistical analysis identified five prototypes molecules, which are capable of explaining 71% of the variance within the inhibitor data set; whilst a further five molecules were also identified as archetypes, describing 75% of data variance. All active corrosion inhibitors, at a 80% threshold, were successfully recognized by the CoMSA model with adequate specificity and precision higher than 70% and 60%, respectively. The model was also capable of identifying structural patterns, that revealed reasonable starting points for where structural changes may augment corrosion inhibition efficacy. The presented methodology can be applied to other functional molecules and extended to cover structure-activity studies in a diverse range of areas such as drug design and novel material discovery. Copyright © 2016 Elsevier Ltd. All rights reserved.

WE-F-BRB-02: Setting the Stage for Incorporation of Toxicity Measures in Treatment Plan Assessments

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

Mayo, C.

2015-06-15

Advancements in informatics in radiotherapy are opening up opportunities to improve our ability to assess treatment plans. Models on individualizing patient dose constraints from prior patient data and shape relationships have been extensively researched and are now making their way into commercial products. New developments in knowledge based treatment planning involve understanding the impact of the radiation dosimetry on the patient. Akin to radiobiology models that have driven intensity modulated radiotherapy optimization, toxicity and outcome predictions based on treatment plans and prior patient experiences may be the next step in knowledge based planning. In order to realize these predictions, itmore » is necessary to understand how the clinical information can be captured, structured and organized with ontologies and databases designed for recall. Large databases containing radiation dosimetry and outcomes present the opportunity to evaluate treatment plans against predictions of toxicity and disease response. Such evaluations can be based on dose volume histogram or even the full 3-dimensional dose distribution and its relation to the critical anatomy. This session will provide an understanding of ontologies and standard terminologies used to capture clinical knowledge into structured databases; How data can be organized and accessed to utilize the knowledge in planning; and examples of research and clinical efforts to incorporate that clinical knowledge into planning for improved care for our patients. Learning Objectives: Understand the role of standard terminologies, ontologies and data organization in oncology Understand methods to capture clinical toxicity and outcomes in a clinical setting Understand opportunities to learn from clinical data and its application to treatment planning Todd McNutt receives funding from Philips, Elekta and Toshiba for some of the work presented.« less

Analysis of a simulation algorithm for direct brain drug delivery

PubMed Central

Rosenbluth, Kathryn Hammond; Eschermann, Jan Felix; Mittermeyer, Gabriele; Thomson, Rowena; Mittermeyer, Stephan; Bankiewicz, Krystof S.

2011-01-01

Convection enhanced delivery (CED) achieves targeted delivery of drugs with a pressure-driven infusion through a cannula placed stereotactically in the brain. This technique bypasses the blood brain barrier and gives precise distributions of drugs, minimizing off-target effects of compounds such as viral vectors for gene therapy or toxic chemotherapy agents. The exact distribution is affected by the cannula positioning, flow rate and underlying tissue structure. This study presents an analysis of a simulation algorithm for predicting the distribution using baseline MRI images acquired prior to inserting the cannula. The MRI images included diffusion tensor imaging (DTI) to estimate the tissue properties. The algorithm was adapted for the devices and protocols identified for upcoming trials and validated with direct MRI visualization of Gadolinium in 20 infusions in non-human primates. We found strong agreement between the size and location of the simulated and gadolinium volumes, demonstrating the clinical utility of this surgical planning algorithm. PMID:21945468

Combinatorial QSAR Modeling of Rat Acute Toxicity by Oral Exposure

EPA Science Inventory

Quantitative Structure-Activity Relationship (QSAR) toxicity models have become popular tools for identifying potential toxic compounds and prioritizing candidates for animal toxicity tests. However, few QSAR studies have successfully modeled large, diverse mammalian toxicity end...

Design and implementation of an open source indexing solution for a large set of radiological reports and images.

PubMed

Voet, T; Devolder, P; Pynoo, B; Vercruysse, J; Duyck, P

2007-11-01

This paper hopes to share the insights we experienced during designing, building, and running an indexing solution for a large set of radiological reports and images in a production environment for more than 3 years. Several technical challenges were encountered and solved in the course of this project. One hundred four million words in 1.8 million radiological reports from 1989 to the present were indexed and became instantaneously searchable in a user-friendly fashion; the median query duration is only 31 ms. Currently, our highly tuned index holds 332,088 unique words in four languages. The indexing system is feature-rich and language-independent and allows for making complex queries. For research and training purposes it certainly is a valuable and convenient addition to our radiology informatics toolbox. Extended use of open-source technology dramatically reduced both implementation time and cost. All software we developed related to the indexing project has been made available to the open-source community covered by an unrestricted Berkeley Software Distribution-style license.

Environmental footprints of brick kiln bottom ashes: Geostatistical approach for assessment of metal toxicity.

PubMed

Mondal, Ananya; Das, Subhasish; Sah, Rajesh Kumar; Bhattacharyya, Pradip; Bhattacharya, Satya Sundar

2017-12-31

Coal fired brick kiln factories generate significant of brick kiln bottom ash (BKBA) that contaminate soil and water environments of areas near the dumping sites through leaching of toxic metals (Pb, Cr, Cd, Zn, Mn, and Cu). However, characteristics and environmental effects of BKBAs are yet unknown. We collected BKBA samples from 32 strategic locations of two rapidly developing States (West Bengal and Assam) of India. Scanning electron microscope images indicated spherical and granular structures of BKBAs produced in West Bengal (WBKBA) and Assam (ABKBA) respectively; while energy dispersive spectroscopy and analytical assessments confirmed substantial occurrence of total organic C and nutrient elements (N, P, K, Ca, Mg, and S) in both the BKBAs. FTIR analysis revealed greater predominance of organic matter in ABKBAs than WBKBAs. Occurrence of toxic metals (Cd, Cr, Pb, Zn, Mn, and Cu) was higher in ABKBAs than in WBKBAs; while organic and residual fractions of metals were highly predominant in most of the BKBAs. Principal component analysis showed that metal contents and pH were the major distinguishing characteristics of the BKBAs generated in the two different environmental locations. Human health risk associated with BKBAs generated in Assam is of significant concern. Finally, geo-statistical tools enabled to predict the spatial distribution patterns of toxic metals contributed by the BKBAs in Assam and West Bengal respectively. Assessment of contamination index, geo-accumulation index, and ecological risk index revealed some BKBAs to be more toxic than others. Copyright © 2017. Published by Elsevier B.V.

Acute toxicity of anionic and non-ionic surfactants to aquatic organisms.

PubMed

Lechuga, M; Fernández-Serrano, M; Jurado, E; Núñez-Olea, J; Ríos, F

2016-03-01

The environmental risk of surfactants requires toxicity measurements. As different test organisms have different sensitivity to the toxics, it is necessary to establish the most appropriate organism to classify the surfactant as very toxic, toxic, harmful or safe, in order to establish the maximum permissible concentrations in aquatic ecosystems. We have determined the toxicity values of various anionic surfactants ether carboxylic derivatives using four test organisms: the freshwater crustacean Daphnia magna, the luminescent bacterium Vibrio fischeri, the microalgae Selenastrum capricornutum (freshwater algae) and Phaeodactylum tricornutum (seawater algae). In addition, in order to compare and classify the different families of surfactants, we have included a compilation of toxicity data of surfactants collected from literature. The results indicated that V. fischeri was more sensitive to the toxic effects of the surfactants than was D. magna or the microalgae, which was the least sensitive. This result shows that the most suitable toxicity assay for surfactants may be the one using V. fischeri. The toxicity data revealed considerable variation in toxicity responses with the structure of the surfactants regardless of the species tested. The toxicity data have been related to the structure of the surfactants, giving a mathematical relationship that helps to predict the toxic potential of a surfactant from its structure. Model-predicted toxicity agreed well with toxicity values reported in the literature for several surfactants previously studied. Predictive models of toxicity is a handy tool for providing a risk assessment that can be useful to establish the toxicity range for each surfactant and the different test organisms in order to select efficient surfactants with a lower impact on the aquatic environment. Copyright © 2015 Elsevier Inc. All rights reserved.

Classification and Dose-Response Characterization of Environmental Chemicals Based On Structured Toxicity Information From ToxRefDB

EPA Science Inventory

Thirty years and over a billion of today’s dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data, within the U.S. Environmental Protection Agency’s...

Quantitative imaging reveals heterogeneous growth dynamics and treatment-dependent residual tumor distributions in a three-dimensional ovarian cancer model

NASA Astrophysics Data System (ADS)

Celli, Jonathan P.; Rizvi, Imran; Evans, Conor L.; Abu-Yousif, Adnan O.; Hasan, Tayyaba

2010-09-01

Three-dimensional tumor models have emerged as valuable in vitro research tools, though the power of such systems as quantitative reporters of tumor growth and treatment response has not been adequately explored. We introduce an approach combining a 3-D model of disseminated ovarian cancer with high-throughput processing of image data for quantification of growth characteristics and cytotoxic response. We developed custom MATLAB routines to analyze longitudinally acquired dark-field microscopy images containing thousands of 3-D nodules. These data reveal a reproducible bimodal log-normal size distribution. Growth behavior is driven by migration and assembly, causing an exponential decay in spatial density concomitant with increasing mean size. At day 10, cultures are treated with either carboplatin or photodynamic therapy (PDT). We quantify size-dependent cytotoxic response for each treatment on a nodule by nodule basis using automated segmentation combined with ratiometric batch-processing of calcein and ethidium bromide fluorescence intensity data (indicating live and dead cells, respectively). Both treatments reduce viability, though carboplatin leaves micronodules largely structurally intact with a size distribution similar to untreated cultures. In contrast, PDT treatment disrupts micronodular structure, causing punctate regions of toxicity, shifting the distribution toward smaller sizes, and potentially increasing vulnerability to subsequent chemotherapeutic treatment.

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

Smith, Euan; Kempson, Ivan; Juhasz, Albert L.

The consumption of arsenic (As) contaminated rice is an important exposure route for humans in countries where rice cultivation employs As contaminated irrigation water. Arsenic toxicity and mobility are a function of its chemical-speciation. The distribution and identification of As in the rice plant are hence necessary to determine the uptake, transformation and potential risk posed by As contaminated rice. In this study we report on the distribution and chemical-speciation of As in rice (Oryza sativa Quest) by X-ray fluorescence (XRF) and X-ray absorption near edge structure (XANES) measurements of rice plants grown in As contaminated paddy water. Investigations ofmore » {mu}XRF images from rice tissues found that As was present in all rice tissues, and its presence correlated with the presence of iron at the root surface and copper in the rice leaf. X-ray absorption near edge structure analysis of rice tissues identified that inorganic As was the predominant form of As in all rice tissues studied, and that arsenite became increasingly dominant in the aerial portion of the rice plant.« less

Developing the "Compendium of Strategies to Reduce Teacher Turnover in the Northeast and Islands Region." A Companion to the Database. Issues & Answers. REL 2008-No. 052

ERIC Educational Resources Information Center

Ellis, Pamela; Grogan, Marian; Levy, Abigail Jurist; Tucker-Seeley, Kevon

2008-01-01

This report provides state-, regional-, and district-level decisionmakers in the Northeast and Islands Region with a description of the "Compendium of Strategies to Reduce Teacher Turnover in the Northeast and Islands Region," a searchable database of selected profiles of retention strategies implemented in Connecticut, Maine,…

Bradbury Science Museum Collections Inventory Photos Disc #5

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

Strohmeyer, Wendy J.

The photos on Bradbury Science Museum Collections Inventory Photos Disc #5 is another in an ongoing effort to catalog all artifacts held by the Museum. Photos will be used as part of the condition report for the artifact, and will become part of the collection record in the collections database for that artifact. The collections database will be publically searchable on the Museum website.

'Bradbury Science Museum Collections Inventory Photos Disc #4

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

Strohmeyer, Wendy J.

The photos on Bradbury Science Museum Collections Inventory Photos Disc #4 is another in an ongoing effort to catalog all artifacts held by the Museum. Photos will be used as part of the condition report for the artifact, and will become part of the collection record in the collections database for that artifact. The collections database will be publically searchable on the Museum website.

Whole genome sequences of the USMARC beef cattle diversity panel v2.9 aligned to the bovine reference genome assembly

USDA-ARS?s Scientific Manuscript database

A searchable and publicly viewable set of mapped genomes from 96 beef sires from 19 popular breeds of U.S. cattle was created. These sires with minimal pedigree relationships, represent >99% of the germplasm used in the US beef industry circa 2000. The group is estimated to contain more than 187 u...

Research and Development of Energetic Ionic Liquids. Next Generation Energetic Materials Striking a Balance between Performance, Insensitivity, and Environmental Sustainability

DTIC Science & Technology

2011-12-01

thermal and catalytic ignition flight qualified and flown (PRISMA) Distribution A: Public Release, Distribution unlimited. AF - M315E is US Air Force IL...for Space Propulsion, Noordwijk, The Netherlands, 20-22 June 2001. 6 Toxicity Assessment of AF - M315E Toxicity Testing Results PROPERTY AF - M315E ...Distribution Unlimited. 8 Much Effort Required in Small- Scale Safety/Hazard Evaluations Propellant AF - M315E * LMP-103S** Unconfined Burn Test 1 and 3: No

Selenium: Poison and Preventive.

ERIC Educational Resources Information Center

Marmion Howe, Sister

1978-01-01

Selenium is an essential nutrient to the human body, but it can reach toxic levels causing a disease called selenosis. This article discusses selenium, its geographical distribution, toxicity, nutritional role, and carcinogenicity. (MA)

In Silico Prediction of Organ Level Toxicity: Linking Chemistry to Adverse Effects

PubMed Central

Cronin, Mark T.D.; Enoch, Steven J.; Mellor, Claire L.; Przybylak, Katarzyna R.; Richarz, Andrea-Nicole; Madden, Judith C.

2017-01-01

In silico methods to predict toxicity include the use of (Quantitative) Structure-Activity Relationships ((Q)SARs) as well as grouping (category formation) allowing for read-across. A challenging area for in silico modelling is the prediction of chronic toxicity and the No Observed (Adverse) Effect Level (NO(A)EL) in particular. A proposed solution to the prediction of chronic toxicity is to consider organ level effects, as opposed to modelling the NO(A)EL itself. This review has focussed on the use of structural alerts to identify potential liver toxicants. In silico profilers, or groups of structural alerts, have been developed based on mechanisms of action and informed by current knowledge of Adverse Outcome Pathways. These profilers are robust and can be coded computationally to allow for prediction. However, they do not cover all mechanisms or modes of liver toxicity and recommendations for the improvement of these approaches are given. PMID:28744348

In Silico Prediction of Organ Level Toxicity: Linking Chemistry to Adverse Effects.

PubMed

Cronin, Mark T D; Enoch, Steven J; Mellor, Claire L; Przybylak, Katarzyna R; Richarz, Andrea-Nicole; Madden, Judith C

2017-07-01

In silico methods to predict toxicity include the use of (Quantitative) Structure-Activity Relationships ((Q)SARs) as well as grouping (category formation) allowing for read-across. A challenging area for in silico modelling is the prediction of chronic toxicity and the No Observed (Adverse) Effect Level (NO(A)EL) in particular. A proposed solution to the prediction of chronic toxicity is to consider organ level effects, as opposed to modelling the NO(A)EL itself. This review has focussed on the use of structural alerts to identify potential liver toxicants. In silico profilers, or groups of structural alerts, have been developed based on mechanisms of action and informed by current knowledge of Adverse Outcome Pathways. These profilers are robust and can be coded computationally to allow for prediction. However, they do not cover all mechanisms or modes of liver toxicity and recommendations for the improvement of these approaches are given.

Modelling the Tox21 10 K chemical profiles for in vivo toxicity prediction and mechanism characterization

PubMed Central

Huang, Ruili; Xia, Menghang; Sakamuru, Srilatha; Zhao, Jinghua; Shahane, Sampada A.; Attene-Ramos, Matias; Zhao, Tongan; Austin, Christopher P.; Simeonov, Anton

2016-01-01

Target-specific, mechanism-oriented in vitro assays post a promising alternative to traditional animal toxicology studies. Here we report the first comprehensive analysis of the Tox21 effort, a large-scale in vitro toxicity screening of chemicals. We test ∼10,000 chemicals in triplicates at 15 concentrations against a panel of nuclear receptor and stress response pathway assays, producing more than 50 million data points. Compound clustering by structure similarity and activity profile similarity across the assays reveals structure–activity relationships that are useful for the generation of mechanistic hypotheses. We apply structural information and activity data to build predictive models for 72 in vivo toxicity end points using a cluster-based approach. Models based on in vitro assay data perform better in predicting human toxicity end points than animal toxicity, while a combination of structural and activity data results in better models than using structure or activity data alone. Our results suggest that in vitro activity profiles can be applied as signatures of compound mechanism of toxicity and used in prioritization for more in-depth toxicological testing. PMID:26811972

Housing and health: intersection of poverty and environmental exposures.

PubMed

Rauh, Virginia A; Landrigan, Philip J; Claudio, Luz

2008-01-01

The importance of adequate housing for the maintenance of health and well-being has long been a topic of scientific and public health policy discussion, but the links remain elusive. Here we explore the role of the residential environment in the etiology of illness (specifically asthma) and the persistence of socioeconomic health disparities. Housing conditions, shaped by social forces, affect exposure to physical and chemical "toxicants," thereby translating social adversities into individual illness and population health disparities. We discuss the mediating role of housing in determining health outcomes at multiple levels (social-structural, neighborhood, and individual family). To date, little attention has been paid by most environmental health scientists to the social-structural conditions underlying gross inequities in the distribution of toxic exposures, with even less attention to the processes whereby these social conditions may directly affect susceptibility to the toxic exposures themselves. This chapter goes beyond traditional medical and environmental science models to incorporate a range of social and physical determinants of environmental pollutions, illustrating how these conditions result in health and illness. We focus here on childhood asthma as an example of a serious public health problem that has been associated with low income, minority status, and characteristics of the home environment. We end the chapter with a discussion of the environmental justice movement and the role of housing as a potential agent of change and focus of interventions aimed to reduce the harmful effects of environmental pollutants.

Electromagnetic-Guided MLC Tracking Radiation Therapy for Prostate Cancer Patients: Prospective Clinical Trial Results.

PubMed

Keall, Paul J; Colvill, Emma; O'Brien, Ricky; Caillet, Vincent; Eade, Thomas; Kneebone, Andrew; Hruby, George; Poulsen, Per R; Zwan, Benjamin; Greer, Peter B; Booth, Jeremy

2018-06-01

To report on the primary and secondary outcomes of a prospective clinical trial of electromagnetic-guided multileaf collimator (MLC) tracking radiation therapy for prostate cancer. Twenty-eight men with prostate cancer were treated with electromagnetic-guided MLC tracking with volumetric modulated arc therapy. A total of 858 fractions were delivered, with the dose per fraction ranging from 2 to 13.75 Gy. The primary outcome was feasibility, with success determined if >95% of fractions were successfully delivered. The secondary outcomes were (1) the improvement in beam-target geometric alignment, (2) the improvement in dosimetric coverage of the prostate and avoidance of critical structures, and (3) no acute grade ≥3 genitourinary or gastrointestinal toxicity. All 858 planned fractions were successfully delivered with MLC tracking, demonstrating the primary outcome of feasibility (P < .001). MLC tracking improved the beam-target geometric alignment from 1.4 to 0.90 mm (root-mean-square error). MLC tracking improved the dosimetric coverage of the prostate and reduced the daily variation in dose to critical structures. No acute grade ≥3 genitourinary or gastrointestinal toxicity was observed. Electromagnetic-guided MLC tracking radiation therapy for prostate cancer is feasible. The patients received improved geometric targeting and delivered dose distributions that were closer to those planned than they would have received without electromagnetic-guided MLC tracking. No significant acute toxicity was observed. Copyright © 2018 Elsevier Inc. All rights reserved.

EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

NASA Technical Reports Server (NTRS)

Johnston, Stephanie S.; Alpert, Brian K.; Montalvo, Edwin James; Welsh, Lawrence Daren; Wray, Scott; Mavridis, Costa

2016-01-01

The EVA Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, easy to search repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision controlled system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, as well as hundreds of others that support the EVA. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

EVA Wiki - Transforming Knowledge Management for EVA Flight Controllers and Instructors

NASA Technical Reports Server (NTRS)

Johnston, Stephanie S.; Alpert, Brian K.; Montalvo, Edwin James; Welsh, Lawrence Daren; Wray, Scott; Mavridis, Costa

2016-01-01

The EVA Wiki was recently implemented as the primary knowledge database to retain critical knowledge and skills in the EVA Operations group at NASA's Johnson Space Center by ensuring that information is recorded in a common, easy to search repository. Prior to the EVA Wiki, information required for EVA flight controllers and instructors was scattered across different sources, including multiple file share directories, SharePoint, individual computers, and paper archives. Many documents were outdated, and data was often difficult to find and distribute. In 2011, a team recognized that these knowledge management problems could be solved by creating an EVA Wiki using MediaWiki, a free and open-source software developed by the Wikimedia Foundation. The EVA Wiki developed into an EVA-specific Wikipedia on an internal NASA server. While the technical implementation of the wiki had many challenges, one of the biggest hurdles came from a cultural shift. Like many enterprise organizations, the EVA Operations group was accustomed to hierarchical data structures and individually-owned documents. Instead of sorting files into various folders, the wiki searches content. Rather than having a single document owner, the wiki harmonized the efforts of many contributors and established an automated revision controlled system. As the group adapted to the wiki, the usefulness of this single portal for information became apparent. It transformed into a useful data mining tool for EVA flight controllers and instructors, as well as hundreds of others that support EVA. Program managers, engineers, astronauts, flight directors, and flight controllers in differing disciplines now have an easier-to-use, searchable system to find EVA data. This paper presents the benefits the EVA Wiki has brought to NASA's EVA community, as well as the cultural challenges it had to overcome.

Spatial and temporal variations in toxicity in a marsh receiving urban runoff

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

Katznelson, R.; Jewell, W.T.; Anderson, S.L.

1993-06-01

This project is composed of two sections. The first section describes dry weather toxicity surveys to evaluate the distribution of toxicity in the waters of San Francisco Bay and adjacent wetland habitat, and the second is a series of wet weather toxicity studies with emphasis on a marsh receiving urban runoff. The dry weather studies are reported in the appendices, while the wet weather work comprises the main report.

Beam Path Toxicities to Non-Target Structures During Intensity-Modulated Radiation Therapy for Head and Neck Cancer

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

Rosenthal, David I.; Chambers, Mark S.; Fuller, Clifton D.

2008-11-01

Background: Intensity-modulated radiation therapy (IMRT) beams traverse nontarget normal structures not irradiated during three-dimensional conformal RT (3D-CRT) for head and neck cancer (HNC). This study estimates the doses and toxicities to nontarget structures during IMRT. Materials and Methods: Oropharyngeal cancer IMRT and 3D-CRT cases were reviewed. Dose-volume histograms (DVH) were used to evaluate radiation dose to the lip, cochlea, brainstem, occipital scalp, and segments of the mandible. Toxicity rates were compared for 3D-CRT, IMRT alone, or IMRT with concurrent cisplatin. Descriptive statistics and exploratory recursive partitioning analysis were used to estimate dose 'breakpoints' associated with observed toxicities. Results: A totalmore » of 160 patients were evaluated for toxicity; 60 had detailed DVH evaluation and 15 had 3D-CRT plan comparison. Comparing IMRT with 3D-CRT, there was significant (p {<=} 0.002) nonparametric differential dose to all clinically significant structures of interest. Thirty percent of IMRT patients had headaches and 40% had occipital scalp alopecia. A total of 76% and 38% of patients treated with IMRT alone had nausea and vomiting, compared with 99% and 68%, respectively, of those with concurrent cisplatin. IMRT had a markedly distinct toxicity profile than 3D-CRT. In recursive partitioning analysis, National Cancer Institute's Common Toxicity Criteria adverse effects 3.0 nausea and vomiting, scalp alopecia and anterior mucositis were associated with reconstructed mean brainstem dose >36 Gy, occipital scalp dose >30 Gy, and anterior mandible dose >34 Gy, respectively. Conclusions: Dose reduction to specified structures during IMRT implies an increased beam path dose to alternate nontarget structures that may result in clinical toxicities that were uncommon with previous, less conformal approaches. These findings have implications for IMRT treatment planning and research, toxicity assessment, and multidisciplinary patient management.« less

Toxicity and tissue distribution of 2,2',4,4'- and 3,3',4, 4'-tetrachlorobiphenyls in houseflies.

PubMed

Saghir, S A; Hansen, L G

1999-02-01

Insects selectively retain different polychlorinated biphenyls (PCBs) which are then contributed to the food chain. To quantitate specific differences, adult female houseflies (Musca domestica L.) were topically dosed with 0.5 microgram of two structurally distinct PCB congeners (14C-2,2',4,4'-tetraCB or 14C-3,3',4,4'-tetraCB). Total radioactivity in the acetone rinse of intact flies, several tissues, and excrement was determined at 11 time points over a 48-h period. Ninety-seven percent of the applied 2,2',4,4'-tetraCB disappeared from the surface following an initial rapid absorption of 79% within 3 h. The absorbed 2,2',4,4'-tetraCB was immediately found within the thoracic cuticle, then spreading laterally to the abdominal cuticle and head, through the wax layers, or penetrating to the alimentary canal and ovaries. Penetration of 3,3',4, 4'-tetraCB was markedly slower; even though 87% of the applied dose was absorbed within 48 h, only 19% of the dose penetrated into the fly body within the first 3 h. This PCB very slowly distributed into the tissues. Toxicities of the sublethal doses were determined by monitoring changes in activity of houseflies following dosing with 0. 5 microg of radioactive PCBs. Flies treated with 2,2',5-triCB and 3, 3',4,4'-tetraCB remained very active, whereas 2,2',4, 4'-tetraCB-treated flies were less active, consistent with the previously reported toxicity of this congener. Copyright 1999 Academic Press.

STRUCTURE-ACTIVITY RELATIONSHIP STUIDES AND THEIR ROLE IN PREDICTING AND INVESTIGATING CHEMICAL TOXICITY

EPA Science Inventory

Structure-Activity Relationship Studies and their Role in Predicting and Investigating Chemical Toxicity

Structure-activity relationships (SAR) represent attempts to generalize chemical information relative to biological activity for the twin purposes of generating insigh...

Synthesis of plant-mediated gold nanoparticles and catalytic role of biomatrix-embedded nanomaterials

PubMed Central

Sharma, Nilesh C.; Nath, Sudip; Parsons, Jason G.; Gardea- Torresdey, Jorge L.; Pal, Tarasankar

2008-01-01

Growth of Sesbania seedlings in chloroaurate solution resulted in the accumulation of gold with the formation of stable gold nanoparticles in plant tissues. Transmission electron microscopy revealed the intracellular distribution of monodisperse nanospheres, possibly due to reduction of the metal ions by secondary metabolites present in cells. X-ray absorption near-edge structure and extended X-ray absorption fine structure demonstrated a high degree of efficiency for the biotransformation of Au(III) into Au(0) by plant tissues. The catalytic function of the nanoparticle-rich biomass was substantiated by the reduction of aqueous 4-nitrophenol (4-NP). This is the first report of gold nanoparticle-bearing biomatrix directly reducing a toxic pollutant, 4-NP. PMID:17711235

The importance of trace element speciation in biomedical science.

PubMed

Templeton, Douglas M

2003-04-01

According to IUPAC terminology, trace element speciation reflects differences in chemical composition at multiple levels from nuclear and electronic structure to macromolecular complexation. In the medical sciences, all levels of composition are important in various circumstances, and each can affect the bioavailability, distribution, physiological function, toxicity, diagnostic utility, and therapeutic potential of an element. Here we discuss, with specific examples, three biological principles in the intimate relation between speciation and biological behavior: i) the kinetics of interconversion of species determines distribution within the organism, ii) speciation governs transport across various biological barriers, and iii) speciation can limit potentially undesirable interactions between physiologically essential elements. We will also describe differences in the speciation of iron in states of iron overload, to illustrate how speciation analysis can provide insight into cellular processes in human disease.

40 CFR 80.820 - What gasoline is subject to the toxics performance requirements of this subpart?

Code of Federal Regulations, 2011 CFR

2011-07-01

... performance requirements of this subpart? 80.820 Section 80.820 Protection of Environment ENVIRONMENTAL... Gasoline Toxics Performance Requirements § 80.820 What gasoline is subject to the toxics performance..., distribution and sale to the ultimate consumer; and (3) The gasoline is not made available for use as motor...

40 CFR 80.820 - What gasoline is subject to the toxics performance requirements of this subpart?

Code of Federal Regulations, 2010 CFR

2010-07-01

... performance requirements of this subpart? 80.820 Section 80.820 Protection of Environment ENVIRONMENTAL... Gasoline Toxics Performance Requirements § 80.820 What gasoline is subject to the toxics performance..., distribution and sale to the ultimate consumer; and (3) The gasoline is not made available for use as motor...

Assessment of environmental risks from toxic and nontoxic stressors; a proposed concept for a risk-based management tool for offshore drilling discharges.

PubMed

Smit, Mathijs G D; Jak, Robbert G; Rye, Henrik; Frost, Tone Karin; Singsaas, Ivar; Karman, Chris C

2008-04-01

In order to improve the ecological status of aquatic systems, both toxic (e.g., chemical) and nontoxic stressors (e.g., suspended particles) should be evaluated. This paper describes an approach to environmental risk assessment of drilling discharges to the sea. These discharges might lead to concentrations of toxic compounds and suspended clay particles in the water compartment and concentrations of toxic compounds, burial of biota, change in sediment structure, and oxygen depletion in marine sediments. The main challenges were to apply existing protocols for environmental risk assessment to nontoxic stressors and to combine risks arising from exposure to these stressors with risk from chemical exposure. The defined approach is based on species sensitivity distributions (SSDs). In addition, precautionary principles from the EU-Technical Guidance Document were incorporated to assure that the method is acceptable in a regulatory context. For all stressors a protocol was defined to construct an SSD for no observed effect concentrations (or levels; NOEC(L)-SSD) to allow for the calculation of the potentially affected fraction of species from predicted exposures. Depending on the availability of data, a NOEC-SSD for toxicants can either be directly based on available NOECs or constructed from the predicted no effect concentration and the variation in sensitivity among species. For nontoxic stressors a NOEL-SSD can be extrapolated from an SSD based on effect or field data. Potentially affected fractions of species at predicted exposures are combined into an overall risk estimate. The developed approach facilitates environmental management of drilling discharges and can be applied to define risk-mitigating measures for both toxic and nontoxic stress.

Structure-based thresholds of toxicological concern-guidance for application to substances present at low levels in the diet

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

Renwick, A.G.

Health-based guidance values, such as the ADI, use chemical-specific data to determine the highest intake that would be without significant adverse health effects. A threshold of toxicological concern (TTC) is a level of intake predicted to be without adverse effects based on the toxicity of structurally related compounds. The main advantage of the use of TTCs is that the risk of low exposures can be evaluated without the need for chemical-specific animal toxicity data. TTCs have been used for many years for screening the safety of packaging migrants by the FDA in the USA, and of flavoring substances, by themore » JECFA. A recent reassessment of the use of TTCs, organized by ILSI Europe, has developed a decision tree which allows a systematic approach to the evaluation of low levels of diverse chemicals in food. The decision tree incorporates a series of increasing TTC values into a step-wise approach. Potentially genotoxic carcinogens are considered first, based on the presence of known structural alerts. Aflatoxin-like, azoxy- and nitroso-compounds are removed from consideration because they are the most potent, and a practical TTC could not be established. Other compounds with structural alerts for genotoxicity are allocated a TTC of 0.15 {mu}g/person per day. Compounds without structural alerts for genotoxicity are evaluated based on chemical structure and intake using a series of TTC values derived by the application of a 100-fold uncertainty factor to the 5th percentile of the distribution of NOAELs from chronic studies on compounds sharing similar structural characteristics.« less

Bioalerts: a python library for the derivation of structural alerts from bioactivity and toxicity data sets.

PubMed

Cortes-Ciriano, Isidro

2016-01-01

Assessing compound toxicity at early stages of the drug discovery process is a crucial task to dismiss drug candidates likely to fail in clinical trials. Screening drug candidates against structural alerts, i.e. chemical fragments associated to a toxicological response prior or after being metabolized (bioactivation), has proved a valuable approach for this task. During the last decades, diverse algorithms have been proposed for the automatic derivation of structural alerts from categorical toxicity data sets. Here, the python library bioalerts is presented, which comprises functionalities for the automatic derivation of structural alerts from categorical (dichotomous), e.g. toxic/non-toxic, and continuous bioactivity data sets, e.g. [Formula: see text] or [Formula: see text] values. The library bioalerts relies on the RDKit implementation of the circular Morgan fingerprint algorithm to compute chemical substructures, which are derived by considering radial atom neighbourhoods of increasing bond radius. In addition to the derivation of structural alerts, bioalerts provides functionalities for the calculation of unhashed (keyed) Morgan fingerprints, which can be used in predictive bioactivity modelling with the advantage of allowing for a chemically meaningful deconvolution of the chemical space. Finally, bioalerts provides functionalities for the easy visualization of the derived structural alerts.

Web-enabled Exercise Generation Tool for Battle Command Training

DTIC Science & Technology

2010-08-01

perceived as fair. Some non-instructional bells and whistles, such as background music and two-dimensional animation, should be judiciously...modify the current image by changing its size or adding a caption (Figure 12). Second, the trainer can upload a new image from his/her computer and...specify properties such as size, caption , image credit, and whether the image is searchable and usable by other trainers (Figure 13). Finally, the

Virtual Evidence Cart - RP (VEC-RP).

PubMed

Liu, Fang; Fontelo, Paul; Muin, Michael; Ackerman, Michael

2005-01-01

VEC-RP (Virtual Evident Cart) is an open, Web-based, searchable collection of clinical questions and relevant references from MEDLINE/PubMed for healthcare professionals. The architecture consists of four parts: clinical questions, relevant articles from MEDLINE/PubMed, "bottom-line" answers, and peer reviews of entries. Only registered users can add reviews but unregistered users can read them. Feedback from physicians, mostly in the Philippines (RP) who tested the system, is positive.

A zebra-band phenotype in maize can be suppressed in constant light, and results from mutation of a PPOXlike gene (protophorphyrinogen oxidase IX-like) for porphyrin biosynthesis

USDA-ARS?s Scientific Manuscript database

A zebra-band phenotype was identified in a maize population of transposon-tagged mutants (UniformMu, searchable by sequence at MaizeGDB.org). Genotype-phenotype analysis of an F2 family showed that the zebra stripes co-segregated with a single Mu insertion in the second exon of a Protoporphyrinogen ...

DEVELOPMENT OF QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIPS (QSARS) TO PREDICT TOXICITY FOR A VARIETY OF HUMAN AND ECOLOGICAL ENDPOINTS

EPA Science Inventory

A web accessible software tool is being developed to predict the toxicity of unknown chemicals for a wide variety of endpoints. The tool will enable a user to easily predict the toxicity of a query compound by simply entering its structure in a 2-dimensional (2-D) chemical sketc...

Secure medical information sharing in cloud computing.

PubMed

Shao, Zhiyi; Yang, Bo; Zhang, Wenzheng; Zhao, Yi; Wu, Zhenqiang; Miao, Meixia

2015-01-01

Medical information sharing is one of the most attractive applications of cloud computing, where searchable encryption is a fascinating solution for securely and conveniently sharing medical data among different medical organizers. However, almost all previous works are designed in symmetric key encryption environment. The only works in public key encryption do not support keyword trapdoor security, have long ciphertext related to the number of receivers, do not support receiver revocation without re-encrypting, and do not preserve the membership of receivers. In this paper, we propose a searchable encryption supporting multiple receivers for medical information sharing based on bilinear maps in public key encryption environment. In the proposed protocol, data owner stores only one copy of his encrypted file and its corresponding encrypted keywords on cloud for multiple designated receivers. The keyword ciphertext is significantly shorter and its length is constant without relation to the number of designated receivers, i.e., for n receivers the ciphertext length is only twice the element length in the group. Only the owner knows that with whom his data is shared, and the access to his data is still under control after having been put on the cloud. We formally prove the security of keyword ciphertext based on the intractability of Bilinear Diffie-Hellman problem and the keyword trapdoor based on Decisional Diffie-Hellman problem.

A user-friendly phytoremediation database: creating the searchable database, the users, and the broader implications.

PubMed

Famulari, Stevie; Witz, Kyla

2015-01-01

Designers, students, teachers, gardeners, farmers, landscape architects, architects, engineers, homeowners, and others have uses for the practice of phytoremediation. This research looks at the creation of a phytoremediation database which is designed for ease of use for a non-scientific user, as well as for students in an educational setting ( http://www.steviefamulari.net/phytoremediation ). During 2012, Environmental Artist & Professor of Landscape Architecture Stevie Famulari, with assistance from Kyla Witz, a landscape architecture student, created an online searchable database designed for high public accessibility. The database is a record of research of plant species that aid in the uptake of contaminants, including metals, organic materials, biodiesels & oils, and radionuclides. The database consists of multiple interconnected indexes categorized into common and scientific plant name, contaminant name, and contaminant type. It includes photographs, hardiness zones, specific plant qualities, full citations to the original research, and other relevant information intended to aid those designing with phytoremediation search for potential plants which may be used to address their site's need. The objective of the terminology section is to remove uncertainty for more inexperienced users, and to clarify terms for a more user-friendly experience. Implications of the work, including education and ease of browsing, as well as use of the database in teaching, are discussed.

An Improvement to a Multi-Client Searchable Encryption Scheme for Boolean Queries.

PubMed

Jiang, Han; Li, Xue; Xu, Qiuliang

2016-12-01

The migration of e-health systems to the cloud computing brings huge benefits, as same as some security risks. Searchable Encryption(SE) is a cryptography encryption scheme that can protect the confidentiality of data and utilize the encrypted data at the same time. The SE scheme proposed by Cash et al. in Crypto2013 and its follow-up work in CCS2013 are most practical SE Scheme that support Boolean queries at present. In their scheme, the data user has to generate the search tokens by the counter number one by one and interact with server repeatedly, until he meets the correct one, or goes through plenty of tokens to illustrate that there is no search result. In this paper, we make an improvement to their scheme. We allow server to send back some information and help the user to generate exact search token in the search phase. In our scheme, there are only two round interaction between server and user, and the search token has [Formula: see text] elements, where n is the keywords number in query expression, and [Formula: see text] is the minimum documents number that contains one of keyword in query expression, and the computation cost of server is [Formula: see text] modular exponentiation operation.

From streets to streams: assessing the toxicity potential of urban sediment by particle size

USGS Publications Warehouse

Corsi, Steven R.; Selbig, William R.; Roger T. Bannerman,; ,

2013-01-01

Urban sediment can act as a transport mechanism for a variety of pollutants to move towards a receiving water body. The concentrations of these pollutants oftentimes exceed levels that are toxic to aquatic organisms. Many treatment structures are designed to capture coarse sediment but do not work well to similarly capture the fines. This study measured concentrations of select trace metals and PAHs in both the silt and sand fractions of urban sediment from four sources: stormwater bed, stormwater suspended, street dirt, and streambed. Concentrations were used to assess the toxic potential of sediment based on published sediment quality guidelines. All sources of sediment showed some level of toxic potential with stormwater bed sediment the highest followed by stormwater suspended, street dirt, and streambed. Both metal and PAH concentration distributions were highly correlated between the four sampling locations suggesting the presence of one or perhaps only a few sources of these pollutants which remain persistent as sediment is transported from street to stream. Comparison to other forms of combustion- and vehicle-related sources of PAHs revealed coal tar sealants to have the strongest correlation, in both the silt and sand fractions, at all four sampling sites. This information is important for environmental managers when selecting the most appropriate Best Management Practice (BMP) as a way to mitigate pollution conveyed in urban stormwater from source to sink.

Reduced-illuminance autofluorescence imaging in ABCA4-associated retinal degenerations

NASA Astrophysics Data System (ADS)

Cideciyan, Artur V.; Swider, Malgorzata; Aleman, Tomas S.; Roman, Marisa I.; Sumaroka, Alexander; Schwartz, Sharon B.; Stone, Edwin M.; Jacobson, Samuel G.

2007-05-01

The health of the retinal pigment epithelium (RPE) can be estimated with autofluorescence (AF) imaging of lipofuscin, which accumulates as a byproduct of retinal exposure to light. Lipofuscin may be toxic to the RPE, and its toxicity may be enhanced by short-wavelength (SW) illumination. The high-intensity and SW excitation light used in conventional AF imaging could, at least in principle, increase the rate of lipofuscin accumulation and/or increase its toxicity. We considered two reduced-illuminance AF imaging (RAFI) methods as alternatives to conventional AF imaging. RAFI methods use either near-infrared (NIR) light or reduced-radiance SW illumination for excitation of fluorophores. We quantified the distribution of RAFI signals in relation to retinal structure and function in patients with the prototypical lipofuscin accumulation disease caused by mutations in ABCA4. There was evidence for two subclinical stages of macular ABCA4 disease involving hyperautofluorescence of both SW- and NIR-RAFI with and without associated loss of visual function. Use of RAFI methods and microperimetry in future clinical trials involving lipofuscinopathies should allow quantification of subclinical disease expression and progression without subjecting the diseased retina/RPE to undue light exposure.

Phorbol esters seed content and distribution in Latin American provenances of Jatropha curcas L.: potential for biopesticide, food and feed.

PubMed

Bueso, Francisco; Sosa, Italo; Chun, Roldan; Pineda, Renan

2016-01-01

Jatropha curcas L. (Jatropha) is believed to have originated from Mexico and Central America. So far, characterization efforts have focused on Asia, Africa and Mexico. Non-toxic, low phorbol ester (PE) varieties have been found only in Mexico. Differences in PE content in seeds and its structural components, crude oil and cake from Jatropha provenances cultivated in Central and South America were evaluated. Seeds were dehulled, and kernels were separated into tegmen, cotyledons and embryo for PE quantitation by RP-HPLC. Crude oil and cake PE content was also measured. No phenotypic departures in seed size and structure were observed among Jatropha cultivated in Central and South America compared to provenances from Mexico, Asia and Africa. Cotyledons comprised 96.2-97.5 %, tegmen 1.6-2.4 % and embryo represented 0.9-1.4 % of dehulled kernel. Total PE content of all nine provenances categorized them as toxic. Significant differences in kernel PE content were observed among provenances from Mexico, Central and South America (P < 0.01), being Mexican the highest (7.6 mg/g) and Cabo Verde the lowest (2.57 mg/g). All accessions had >95 % of PEs concentrated in cotyledons, 0.5-3 % in the tegmen and 0.5-1 % in the embryo. Over 60 % of total PE in dehulled kernels accumulated in the crude oil, while 35-40 % remained in the cake after extraction. Low phenotypic variability in seed physical, structural traits and PE content was observed among provenances from Latin America. Very high-PE provenances with potential as biopesticide were found in Central America. No PE-free, edible Jatropha was found among provenances currently cultivated in Central America and Brazil that could be used for human consumption and feedstock. Furthermore, dehulled kernel structural parts as well as its crude oil and cake contained toxic PE levels.

Caenorhabditis elegans as an alternative in vivo model to determine oral uptake, nanotoxicity, and efficacy of melatonin-loaded lipid-core nanocapsules on paraquat damage

PubMed Central

Charão, Mariele Feiffer; Souto, Caroline; Brucker, Natália; Barth, Anelise; Jornada, Denise S; Fagundez, Daiandra; Ávila, Daiana Silva; Eifler-Lima, Vera L; Guterres, Silvia S; Pohlmann, Adriana R; Garcia, Solange Cristina

2015-01-01

Caenorhabditis elegans is an alternative in vivo model that is being successfully used to assess the pharmacological and toxic effects of drugs. The exponential growth of nanotechnology requires the use of alternative in vivo models to assess the toxic effects of theses nanomaterials. The use of polymeric nanocapsules has shown promising results for drug delivery. Moreover, these formulations have not been used in cases of intoxication, such as in treatment of paraquat (PQ) poisoning. Thus, the use of drugs with properties improved by nanotechnology is a promising approach to overcome the toxic effects of PQ. This research aimed to evaluate the absorption of rhodamine B-labeled melatonin (Mel)-loaded lipid-core nanocapsules (LNC) by C. elegans, the application of this model in nanotoxicology, and the protection of Mel-LNC against PQ damage. The formulations were prepared by self-assembly and characterized by particle sizing, zeta potential, drug content, and encapsulation efficiency. The results demonstrated that the formulations had narrow size distributions. Rhodamine B-labeled Mel-LNC were orally absorbed and distributed in the worms. The toxicity assessment of LNC showed a lethal dose 50% near the highest dose tested, indicating low toxicity of the nanocapsules. Moreover, pretreatment with Mel-LNC significantly increased the survival rate, reduced the reactive oxygen species, and maintained the development in C. elegans exposed to PQ compared to those worms that were either untreated or pretreated with free Mel. These results demonstrated for the first time the uptake and distribution of Mel-LNC by a nematode, and indicate that while LNC is not toxic, Mel-LNC prevents the effects of PQ poisoning. Thus, C. elegans may be an interesting alternative model to test the nanocapsules toxicity and efficacy. PMID:26300641

Synthesis and characterization of mesoporous ZnS with narrow size distribution of small pores

NASA Astrophysics Data System (ADS)

Nistor, L. C.; Mateescu, C. D.; Birjega, R.; Nistor, S. V.

2008-08-01

Pure, nanocrystalline cubic ZnS forming a stable mesoporous structure was synthesized at room temperature by a non-toxic surfactant-assisted liquid liquid reaction, in the 9.5 10.5 pH range of values. The appearance of an X-ray diffraction (XRD) peak in the region of very small angles (˜ 2°) reveals the presence of a porous material with a narrow pore size distribution, but with an irregular arrangement of the pores, a so-called worm hole or sponge-like material. The analysis of the wide angle XRD diffractograms shows the building blocks to be ZnS nanocrystals with cubic structure and average diameter of 2 nm. Transmission electron microscopy (TEM) investigations confirm the XRD results; ZnS crystallites of 2.5 nm with cubic (blende) structure are the building blocks of the pore walls with pore sizes from 1.9 to 2.5 nm, and a broader size distribution for samples with smaller pores. Textural measurements (N2 adsorption desorption isotherms) confirm the presence of mesoporous ZnS with a narrow range of small pore sizes. The relatively lower surface area of around 100 m2/g is attributed to some remaining organic molecules, which are filling the smallest pores. Their presence, confirmed by IR spectroscopy, seems to be responsible for the high stability of the resulting mesoporous ZnS as well.

Different strategies of cadmium detoxification in the submerged macrophyte Ceratophyllum demersum L.

PubMed

Andresen, Elisa; Mattusch, Jürgen; Wellenreuther, Gerd; Thomas, George; Arroyo Abad, Uriel; Küpper, Hendrik

2013-10-01

The heavy metal cadmium (Cd) is highly toxic to plants. To understand the mechanisms of tolerance and resistance to Cd, we treated the rootless, submerged macrophyte Ceratophyllum demersum L. with sub-micromolar concentrations of Cd under environmentally relevant conditions. X-ray fluorescence measurements revealed changing distribution patterns of Cd and Zn at non-toxic (0.2 nM, 2 nM), moderately toxic (20 nM) and highly toxic (200 nM) levels of Cd. Increasing Cd concentrations led to enhanced sequestration of Cd into non-photosynthetic tissues like epidermis and vein. At toxic Cd concentrations, Zn was redistributed and mainly found in the vein. Cd treatment induced the synthesis of phytochelatins (PCs) in the plants, with a threshold of induction already at 20 nM Cd for PC3. In comparison, in plants treated with Cu, elevated PC levels were detected only at the highest concentrations (100-200 nM Cu). Our results show that also non-accumulators like C. demersum store toxic metals in tissues where the heavy metal interferes least with metabolic pathways, but remaining toxicity interferes with micronutrient distribution. Furthermore, we found that the induction of phytochelatins is not proportional to metal concentration, but has a distinct threshold, specific for each PC species. Finally we could show that 20 nM Cd, which was previously regarded as non-toxic to most plants, already induces detoxifying mechanisms.

Toxicity Estimation Software Tool (TEST)

EPA Science Inventory

The Toxicity Estimation Software Tool (TEST) was developed to allow users to easily estimate the toxicity of chemicals using Quantitative Structure Activity Relationships (QSARs) methodologies. QSARs are mathematical models used to predict measures of toxicity from the physical c...

Influence of oyster culture on biogeochemistry and bacterial community structure at the sediment-water interface.

PubMed

Azandégbé, Afi; Poly, Franck; Andrieux-Loyer, Françoise; Kérouel, Roger; Philippon, Xavier; Nicolas, Jean-Louis

2012-10-01

Bacterial community structure and some biogeochemical parameters were studied in the sediment of two Pacific oyster farming sites, Aber Benoît (AB) and Rivière d'Auray (RA) in Brittany (France), to examine the ecological impact of oysters and to evaluate the emission of sulfide and ammonia from sediment. At AB, the organic matter accumulated in the sediment beneath the oyster tables was rapidly mineralized, with strong fluxes of ammonia and sulfide that reached 1014 and 215 μmol m(-2) h(-1), respectively, in June 2007. At RA, the fluxes were about half as strong on average and better distributed through the year. The ammonia and sulfide concentrations in the overlying water never reached levels that would be toxic to oysters in either site, nor did hypoxia occur. Total culturable bacteria (TCB) varied greatly according to the temperature: from 1.6 × 10(4) to 9.4 × 10(7) cell g(-1) sediment. Inversely, the bacterial community structure remained surprising stable through the seasons, marginally influenced by the presence of oysters and by temperature. Bacterial communities appeared to be characteristic of the sites, with only one common phylotype, Vibrio aestuarianus, a potential oyster pathogen. These data refine the hypothesis of seawater toxicity to oysters because of ammonia and sulfide fluxes and show that the measured environmental factors had only a weak influence on bacterial community structure. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

A Predictive Model for Toxicity Effects Assessment of Biotransformed Hepatic Drugs Using Iterative Sampling Method.

PubMed

Tharwat, Alaa; Moemen, Yasmine S; Hassanien, Aboul Ella

2016-12-09

Measuring toxicity is one of the main steps in drug development. Hence, there is a high demand for computational models to predict the toxicity effects of the potential drugs. In this study, we used a dataset, which consists of four toxicity effects:mutagenic, tumorigenic, irritant and reproductive effects. The proposed model consists of three phases. In the first phase, rough set-based methods are used to select the most discriminative features for reducing the classification time and improving the classification performance. Due to the imbalanced class distribution, in the second phase, different sampling methods such as Random Under-Sampling, Random Over-Sampling and Synthetic Minority Oversampling Technique are used to solve the problem of imbalanced datasets. ITerative Sampling (ITS) method is proposed to avoid the limitations of those methods. ITS method has two steps. The first step (sampling step) iteratively modifies the prior distribution of the minority and majority classes. In the second step, a data cleaning method is used to remove the overlapping that is produced from the first step. In the third phase, Bagging classifier is used to classify an unknown drug into toxic or non-toxic. The experimental results proved that the proposed model performed well in classifying the unknown samples according to all toxic effects in the imbalanced datasets.

A possible link between Balkan endemic nephropathy and the leaching of toxic organic compounds from Pliocene lignite by groundwater: Preliminary investigation

USGS Publications Warehouse

Orem, W.H.; Feder, G.L.; Finkelman, R.B.

1999-01-01

Balkan endemic nephropathy (BEN) is a fatal kidney disease that is known to occur only in clusters of villages in alluvial valleys of tributaries of the Danube River in Bulgaria, Romania, Yugoslavia, Bosnia, and Croatia. The confinement of this disease to a specific geographic area has led to speculation that an environmental factor may be involved in the etiology of BEN. Numerous environmental factors have been suggested as causative agents for producing BEN, including toxic metals in drinking water, metal deficiency in soils of BEN areas, and environmental mycotoxins to name a few. These hypotheses have either been disproved or have failed to conclusively demonstrate a connection to the etiology of BEN, or the clustering of BEN villages. In previous work, we observed a distinct geographic relationship between the distribution of Pliocene lignites in the Balkans and BEN villages. We hypothesized that the long-term consumption of well water containing toxic organic compounds derived from the leaching of nearby Pliocene lignites by groundwater was a primary factor in the etiology of BEN. In our current work, chemical analysis using 13C nuclear magnetic resonance (13CNMR) spectroscopy indicated a high degree of organic functionality in Pliocene lignite from the Balkans, and suggested that groundwater can readily leach organic matter from these coal beds. Semi-quantitative gas chromatography/mass spectroscopy analysis of solvent extracts of groundwater from shallow wells in BEN villages indicated the presence of potentially toxic aromatic compounds, such as napthalene, fluorene, phenanthrene, and pyrene at concentrations in the ppb range. Laboratory leaching of Balkan Pliocene lignites with distilled water yielded soluble organic matter (> 500 MW) containing large amounts of aromatic structures similar to the simple/discrete aromatic compounds detected in well water from BEN villages. These preliminary results are permissive of our hypothesis and suggest that further work on the possible relationship between the etiology of BEN and toxic aromatic substances leached from Pliocene lignites in well water is warranted.A distinct geographic relationship between the distribution of Pliocene lignites in the Balkans and villages where Balkan endemic nephropathy (BEN) occurs has been observed, indicating a possible link between BEN and the long-term consumption of well water containing toxic organic compounds derived from the leaching of nearby Pliocene lignites. Preliminary investigations by NMR spectroscopy, gas chromatography/mass spectroscopy and leaching experiments show a high degree of organic functionality in the Pliocene lignites, high-leachability by groundwater of organic matter from these beds, and the presence of toxic aromatic compounds.

An in silico algal toxicity model with a wide applicability potential for industrial chemicals and pharmaceuticals.

PubMed

Önlü, Serli; Saçan, Melek Türker

2017-04-01

The authors modeled the 72-h algal toxicity data of hundreds of chemicals with different modes of action as a function of chemical structures. They developed mode of action-based local quantitative structure-toxicity relationship (QSTR) models for nonpolar and polar narcotics as well as a global QSTR model with a wide applicability potential for industrial chemicals and pharmaceuticals. The present study rigorously evaluated the generated models, meeting the Organisation for Economic Co-operation and Development principles of robustness, validity, and transparency. The proposed global model had a broad structural coverage for the toxicity prediction of diverse chemicals (some of which are high-production volume chemicals) with no experimental toxicity data. The global model is potentially useful for endpoint predictions, the evaluation of algal toxicity screening, and the prioritization of chemicals, as well as for the decision of further testing and the development of risk-management measures in a scientific and regulatory frame. Environ Toxicol Chem 2017;36:1012-1019. © 2016 SETAC. © 2016 SETAC.

Automated extraction of chemical structure information from digital raster images

PubMed Central

Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

2009-01-01

Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links to scientific research articles. PMID:19196483

[Advance in study on zearalenone's toxicity and determination].

PubMed

He, Qing-Hua; Xu, Yang

2005-07-01

The article is intended to introduce the zearalenone's toxicity, determination methods and prevention. Zearalenone is one of the most widely distributed mycotoxins produces by Fusarium Species, it is harm to animals and human. And it can induce human liver cancer,carcinoma of tesis esophagus cancer. Now we use high-performance liquid chromatography, gas chromatography, thin layer chromatography, non-toxicity determinations to detect it.

Reduced Toxicity, High Performance Monopropellant at the U.S. Air Force Research Laboratory

DTIC Science & Technology

2010-04-27

develop reduced toxicity monopropellant formulations to replace spacecraft hydrazine monopropellant. The Air Force Research Laboratory’s (AFRL’s...Public Release, Distribution unlimited REDUCED TOXICITY, HIGH PERFORMANCE MONOPROPELLANT AT THE U.S. AIR FORCE RESEARCH LABORATORY T.W. Hawkins...information, including suggestions for reducing this burden to Department of Defense, Washington Headquarters Services, Directorate for Information Operations

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

Zheng, Y; Rana, S; Larson, G

Purpose: To analyze the toxicity of uniform scanning proton therapy for lung cancer patients and its correlation with dose distribution. Methods: In this study, we analyzed the toxicity of 128 lung cancer patients, including 18 small cell lung cancer and 110 non small cell lung cancer patients. Each patient was treated with uniform scanning proton beams at our center using typically 2–4 fields. The prescription was typically 74 Cobalt gray equivalent (CGE) at 2 CGE per fraction. 4D Computerized Tomography (CT) scans were used to evaluate the target motion and contour the internal target volume, and repeated 3 times duringmore » the course of treatment to evaluate the need for plan adaptation. Toxicity data for these patients were obtained from the proton collaborative group (PCG) database. For cases of grade 3 toxicities or toxicities of interest such as esophagitis and radiation dermatitis, dose distributions were reviewed and analyzed in attempt to correlate the toxicity with radiation dose. Results: At a median follow up time of about 21 months, none of the patients had experienced Grade 4 or 5 toxicity. The most common adverse effect was dermatitis (81%: 52%-Grade 1, 28%-Grade 2, and 1% Grade 3), followed by fatigue (48%), Cough (46%), and Esophagitis (45%), as shown in Figure 1. Severe toxicities, such as Grade 3 dermatitis or pain of skin, had a clear correlation with high radiation dose. Conclusion: Uniform scanning proton therapy is well tolerated by lung cancer patients. Preliminary analysis indicates there is correlation between severe toxicity and high radiation dose. Understanding of radiation resulted toxicities and careful choice of beam arrangement are critical in minimizing toxicity of skin and other organs.« less

Performance of a sand filter in removal of micro-algae from seawater in aquaculture production systems.

PubMed

Sabiri, N E; Castaing, J B; Massé, A; Jaouen, P

2012-01-01

In this study, a sand filter was used to remove micro-algae from seawater feeding aquaculture ponds. A lab-scale sand filter was used to filter 30,000 cells/mL of Heterocapsa triquetra suspension, a non-toxic micro-alga that has morphological and dimensional (15-20 microm) similarities with Alexandrium sp., one of the smallest toxic micro-algae in seawater. Removal efficiency and capture mechanisms for a fixed superficial velocity (3.5 m/h) were evaluated in relation to size distribution and mean diameter of the sand. Various sands (average diameter ranging between 200 microm and 600 microm) were characterized and used as porous media. The structural parameters of the fixed beds were evaluated for each medium using experimental measurements of pressure drop as a function of superficial velocity over a range of Reynolds numbers covering Darcy's regime and the inertial regime. For a filtration cycle of six hours, the best efficiency (E = 90%) was obtained with the following sand characteristics: sieved sand with a range of grain diameter of 100 and 300 microm and a mean grain diameter equal to 256 microm. Results obtained show the influence of the size distribution of sand on the quality of retention of the micro-algae studied.

TOWARDS REFINED USE OF TOXICITY DATA IN ...

EPA Pesticide Factsheets

In 2003, an International Life Sciences Institute (ILSI) Working Group examined the potential of statistically based structure-activity relationship (SAR) models for use in screening environmental contaminants for possible developmental toxicants. In 2003, an International Life Sciences Institute (ILSI) Working Group examined the potential of statistically based structure-activity relationship (SAR) models for use in screening environmental contaminants for possible developmental toxicants.

A new simple method with high precision for determining the toxicity of antifouling paints on brine shrimp larvae (Artemia): first results.

PubMed

Castritsi-Catharios, J; Bourdaniotis, N; Persoone, G

2007-04-01

The use of antifouling paints is the only truly effective method for the protection of underwater structures from the development of fouling organisms. In the present study, the surface to volume concept constitutes the basis for the development of a new and improved method for determining the toxicity of antifouling paints on marine organisms. Particular emphasis is placed on the attainment of a standardized uniformity of coated surfaces. Failure to control the thickness of the coat of paint in previous studies of this type, has led to inaccurate evaluation of the relative toxicity of samples. Herein, an attempt is made to solve this problem using a simple technique which gives completely uniform and smooth surfaces. The effectiveness of this technique is assessed through two series of experiments using two different types of test containers: 50 ml modified syringes and 7 ml multiwells. The results of the toxicity experiments follow a normal distribution around the average value which allows to consider these values as reliable for comparison of the level of toxic effect detected with the two types of test containers. The mean lethal concentration L(S/V)(50) in the test series conducted in the multiwells (20.38 mm(2)ml(-1)) does not differ significantly from that obtained in the test series using modified syringes (20.065 mm(2)ml(-1)). It can thus be concluded from this preliminary study that the new method and the two different ways of exposing the test organisms to the antifouling paints and their leachates gave reliable and replicable results.

Toxic releases and risk disparity: a spatiotemporal model of industrial ecology and social empowerment.

PubMed

Aoyagi, Hannah; Ogunseitan, Oladele A

2015-06-02

Information-based regulations (IBRs) are founded on the theoretical premise that public participation in accomplishing policy goals is empowered by open access to information. Since its inception in 1988, the Toxics Release Inventory (TRI) has provided the framework and regulatory impetus for the compilation and distribution of data on toxic releases associated with industrial development, following the tenets of IBR. As TRI emissions are reputed to disproportionately affect low-income communities, we investigated how demographic characteristics are related to change in TRI emissions and toxicity risks between 1989 and 2002, and we sought to identify factors that predict these changes. We used local indicators of spatial association (LISA) maps and spatial regression techniques to study risk disparity in the Los Angeles urban area. We also surveyed 203 individuals in eight communities in the same region to measure the levels of awareness of TRI, attitudes towards air pollution, and general environmental risk. We discovered, through spatial lag models, that changes in gross and toxic emissions are related to community ethnic composition, poverty level, home ownership, and base 1989 emissions (R-square=0.034-0.083). We generated a structural equation model to explain the determinants of social empowerment to act on the basis of environmental information. Hierarchical confirmatory factor analysis (HCFA) supports the theoretical model that individual empowerment is predicted by risk perception, worry, and awareness (Chi-square=63.315, p=0.022, df=42). This study provides strong evidence that spatiotemporal changes in regional-scale environmental risks are influenced by individual-scale empowerment mediated by IBRs.

Toxic Releases and Risk Disparity: A Spatiotemporal Model of Industrial Ecology and Social Empowerment

PubMed Central

Aoyagi, Hannah; Ogunseitan, Oladele A.

2015-01-01

Information-based regulations (IBRs) are founded on the theoretical premise that public participation in accomplishing policy goals is empowered by open access to information. Since its inception in 1988, the Toxics Release Inventory (TRI) has provided the framework and regulatory impetus for the compilation and distribution of data on toxic releases associated with industrial development, following the tenets of IBR. As TRI emissions are reputed to disproportionately affect low-income communities, we investigated how demographic characteristics are related to change in TRI emissions and toxicity risks between 1989 and 2002, and we sought to identify factors that predict these changes. We used local indicators of spatial association (LISA) maps and spatial regression techniques to study risk disparity in the Los Angeles urban area. We also surveyed 203 individuals in eight communities in the same region to measure the levels of awareness of TRI, attitudes towards air pollution, and general environmental risk. We discovered, through spatial lag models, that changes in gross and toxic emissions are related to community ethnic composition, poverty level, home ownership, and base 1989 emissions (R-square = 0.034–0.083). We generated a structural equation model to explain the determinants of social empowerment to act on the basis of environmental information. Hierarchical confirmatory factor analysis (HCFA) supports the theoretical model that individual empowerment is predicted by risk perception, worry, and awareness (Chi-square = 63.315, p = 0.022, df = 42). This study provides strong evidence that spatiotemporal changes in regional-scale environmental risks are influenced by individual-scale empowerment mediated by IBRs. PMID:26042368

Fumigant toxicity of cassia and cinnamon oils and cinnamaldehyde and structurally related compounds to Dermanyssus gallinae (Acari: Dermanyssidae).

PubMed

Na, Young Eun; Kim, Soon-Il; Bang, Hea-Son; Kim, Byung-Seok; Ahn, Young-Joon

2011-06-10

The toxicity of two cassia oils, four cinnamon oils and (E)-cinnamaldehyde and (E)-cinnamic acid and 34 structurally related compounds to adult Dermanyssus gallinae (De Geer) collected from a poultry house was examined using a vapour-phase mortality bioassay. Results were compared with those of dichlorvos, a conventional acaricide. The cassia and cinnamon oils (cinnamon technical, cinnamon #500, cassia especial, cassia true, cinnamon bark and cinnamon green leaf) exhibited good fumigant toxicity (LD(50), 11.79-26.40 μg cm(-3)). α-Methyl-(E)-cinnamaldehyde (LD(50), 0.45 μg cm(-3)) and (E)-cinnamaldehyde (0.54 μg cm(-3)) were the most toxic compounds and the toxicity of these compounds was comparable to that of dichlorvos (0.30 μg cm(-3)). Potent fumigant toxicity was also observed in allyl cinnamate, ethyl-α-cyanocinnamate, (E)-2-methoxylcinnamic acid and (Z)-2-methoxylcinnamic acid (LD(50), 0.81-0.92 μg cm(-3)). Structure-activity relationships indicate that structural characteristics, such as types of functional groups and carbon skeleton rather than vapour pressure parameter, appear to play a role in determining toxicity. The essential oils and compounds described merit further study as potential acaricides for the control of D. gallinae populations as fumigants with contact action due to global efforts to reduce the level of highly toxic synthetic acaricides in the agricultural environment. Copyright © 2011. Published by Elsevier B.V.

Monomeric Aβ1–40 and Aβ1–42 Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil

PubMed Central

2016-01-01

The pathogenesis of Alzheimer’s disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ1–40 and Aβ1–42 into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ1–42 compared to that of Aβ1–40 are poorly understood. To explore in detail the structural propensity of the monomeric Aβ1–40 and Aβ1–42 peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ1–40 and Aβ1–42 peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings (3JHNHα, 3JC′C′, 3JC′Hα, 1JHαCα, 2JNCα, and 1JNCα) recorded for Aβ1–40 were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ1–42, suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process. PMID:26780756

Monomeric Aβ(1-40) and Aβ(1-42) Peptides in Solution Adopt Very Similar Ramachandran Map Distributions That Closely Resemble Random Coil.

PubMed

Roche, Julien; Shen, Yang; Lee, Jung Ho; Ying, Jinfa; Bax, Ad

2016-02-09

The pathogenesis of Alzheimer's disease is characterized by the aggregation and fibrillation of amyloid peptides Aβ(1-40) and Aβ(1-42) into amyloid plaques. Despite strong potential therapeutic interest, the structural pathways associated with the conversion of monomeric Aβ peptides into oligomeric species remain largely unknown. In particular, the higher aggregation propensity and associated toxicity of Aβ(1-42) compared to that of Aβ(1-40) are poorly understood. To explore in detail the structural propensity of the monomeric Aβ(1-40) and Aβ(1-42) peptides in solution, we recorded a large set of nuclear magnetic resonance (NMR) parameters, including chemical shifts, nuclear Overhauser effects (NOEs), and J couplings. Systematic comparisons show that at neutral pH the Aβ(1-40) and Aβ(1-42) peptides populate almost indistinguishable coil-like conformations. Nuclear Overhauser effect spectra collected at very high resolution remove assignment ambiguities and show no long-range NOE contacts. Six sets of backbone J couplings ((3)JHNHα, (3)JC'C', (3)JC'Hα, (1)JHαCα, (2)JNCα, and (1)JNCα) recorded for Aβ(1-40) were used as input for the recently developed MERA Ramachandran map analysis, yielding residue-specific backbone ϕ/ψ torsion angle distributions that closely resemble random coil distributions, the absence of a significantly elevated propensity for β-conformations in the C-terminal region of the peptide, and a small but distinct propensity for αL at K28. Our results suggest that the self-association of Aβ peptides into toxic oligomers is not driven by elevated propensities of the monomeric species to adopt β-strand-like conformations. Instead, the accelerated disappearance of Aβ NMR signals in D2O over H2O, particularly pronounced for Aβ(1-42), suggests that intermolecular interactions between the hydrophobic regions of the peptide dominate the aggregation process.

Toxicity and bioconcentration of hexachlorocyclohexane (HCH) in an air-breathing catfish, Saccobranchus fossilis (Bloch)

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

Khangarot, B.S.; Takroo, R.; Singh, R.R.

1991-12-01

The current study was undertaken to determine the sublethal toxicity of commercial grade hexachlorocyclohexane (HCH) to a freshwater air-breathing catfish, Saccobranchus fossilis (Bloch) for 14 days. The bioconcentration of HCH and its distribution in gill, brain and liver was determined. This species was selected for the present study because it is widely distributed in ponds, lakes and rivers of India and consumed as human diet in many parts of the world.

R&D of Energetic Ionic Liquids

DTIC Science & Technology

2011-11-01

Ammonia 3-6 H2O balance Properties LMP-103S AF - M315E Hydrazine Ispvac,lbf sec/lbm (e = 50:1 Pc = 300 psi) 252 (theor.) 235 (del) 266...Distribution A: Public Release, Distribution unlimited. AF - M315E is US Air Force IL-Based Monopropellant •Significant physical property and performance...6 Toxicity Assessment of AF - M315E Toxicity Testing Results PROPERTY AF - M315E HYDRAZINE LD50 (rat), mg/kg 550 60 Dermal Irritation (rabbit

A community dataspace for distribution and processing of "long tail" high resolution topography data

NASA Astrophysics Data System (ADS)

Crosby, C. J.; Nandigam, V.; Arrowsmith, R.

2016-12-01

Topography is a fundamental observable for Earth and environmental science and engineering. High resolution topography (HRT) is revolutionary for Earth science. Cyberinfrastructure that enables users to discover, manage, share, and process these data increases the impact of investments in data collection and catalyzes scientific discovery.National Science Foundation funded OpenTopography (OT, www.opentopography.org) employs cyberinfrastructure that includes large-scale data management, high-performance computing, and service-oriented architectures, providing researchers with efficient online access to large, HRT (mostly lidar) datasets, metadata, and processing tools. HRT data are collected from satellite, airborne, and terrestrial platforms at increasingly finer resolutions, greater accuracy, and shorter repeat times. There has been a steady increase in OT data holdings due to partnerships and collaborations with various organizations with the academic NSF domain and beyond.With the decreasing costs of HRT data collection, via methods such as Structure from Motion, the number of researchers collecting these data is increasing. Researchers collecting these "long- tail" topography data (of modest size but great value) face an impediment, especially with costs associated in making them widely discoverable, shared, annotated, cited, managed and archived. Also because there are no existing central repositories or services to support storage and curation of these datasets, much of it is isolated and difficult to locate and preserve. To overcome these barriers and provide efficient centralized access to these high impact datasets, OT is developing a "Community DataSpace", a service built on a low cost storage cloud, (e.g. AWS S3) to make it easy for researchers to upload, curate, annotate and distribute their datasets. The system's ingestion workflow will extract metadata from data uploaded; validate it; assign a digital object identifier (DOI); and create a searchable catalog entry, before publishing via the OT portal. The OT Community DataSpace will enable wider discovery and utilization of these datasets via the OT portal and sources that federate the OT data catalog (e.g. data.gov), promote citations and more importantly increase the impact of investments in these data.

Tissue distribution and acute toxicity of silver after single intravenous administration in mice: nano-specific and size-dependent effects.

PubMed

Recordati, Camilla; De Maglie, Marcella; Bianchessi, Silvia; Argentiere, Simona; Cella, Claudia; Mattiello, Silvana; Cubadda, Francesco; Aureli, Federica; D'Amato, Marilena; Raggi, Andrea; Lenardi, Cristina; Milani, Paolo; Scanziani, Eugenio

2016-02-29

Silver nanoparticles (AgNPs) are an important class of nanomaterials used as antimicrobial agents for a wide range of medical and industrial applications. However toxicity of AgNPs and impact of their physicochemical characteristics in in vivo models still need to be comprehensively characterized. The aim of this study was to investigate the effect of size and coating on tissue distribution and toxicity of AgNPs after intravenous administration in mice, and compare the results with those obtained after silver acetate administration. Male CD-1(ICR) mice were intravenously injected with AgNPs of different sizes (10 nm, 40 nm, 100 nm), citrate-or polyvinylpyrrolidone-coated, at a single dose of 10 mg/kg bw. An equivalent dose of silver ions was administered as silver acetate. Mice were euthanized 24 h after the treatment, and silver quantification by ICP-MS and histopathology were performed on spleen, liver, lungs, kidneys, brain, and blood. For all particle sizes, regardless of their coating, the highest silver concentrations were found in the spleen and liver, followed by lung, kidney, and brain. Silver concentrations were significantly higher in the spleen, lung, kidney, brain, and blood of mice treated with 10 nm AgNPs than those treated with larger particles. Relevant toxic effects (midzonal hepatocellular necrosis, gall bladder hemorrhage) were found in mice treated with 10 nm AgNPs, while in mice treated with 40 nm and 100 nm AgNPs lesions were milder or negligible, respectively. In mice treated with silver acetate, silver concentrations were significantly lower in the spleen and lung, and higher in the kidney than in mice treated with 10 nm AgNPs, and a different target organ of toxicity was identified (kidney). Administration of the smallest (10 nm) nanoparticles resulted in enhanced silver tissue distribution and overt hepatobiliary toxicity compared to larger ones (40 and 100 nm), while coating had no relevant impact. Distinct patterns of tissue distribution and toxicity were observed after silver acetate administration. It is concluded that if AgNPs become systemically available, they behave differently from ionic silver, exerting distinct and size-dependent effects, strictly related to the nanoparticulate form.

Time-resolved studies define the nature of toxic IAPP intermediates, providing insight for anti-amyloidosis therapeutics

PubMed Central

Abedini, Andisheh; Plesner, Annette; Cao, Ping; Ridgway, Zachary; Zhang, Jinghua; Tu, Ling-Hsien; Middleton, Chris T; Chao, Brian; Sartori, Daniel J; Meng, Fanling; Wang, Hui; Wong, Amy G; Zanni, Martin T; Verchere, C Bruce; Raleigh, Daniel P; Schmidt, Ann Marie

2016-01-01

Islet amyloidosis by IAPP contributes to pancreatic β-cell death in diabetes, but the nature of toxic IAPP species remains elusive. Using concurrent time-resolved biophysical and biological measurements, we define the toxic species produced during IAPP amyloid formation and link their properties to induction of rat INS-1 β-cell and murine islet toxicity. These globally flexible, low order oligomers upregulate pro-inflammatory markers and induce reactive oxygen species. They do not bind 1-anilnonaphthalene-8-sulphonic acid and lack extensive β-sheet structure. Aromatic interactions modulate, but are not required for toxicity. Not all IAPP oligomers are toxic; toxicity depends on their partially structured conformational states. Some anti-amyloid agents paradoxically prolong cytotoxicity by prolonging the lifetime of the toxic species. The data highlight the distinguishing properties of toxic IAPP oligomers and the common features that they share with toxic species reported for other amyloidogenic polypeptides, providing information for rational drug design to treat IAPP induced β-cell death. DOI: http://dx.doi.org/10.7554/eLife.12977.001 PMID:27213520

A Novel Concept for the Search and Retrieval of the Derwent Markush Resource Database.

PubMed

Barth, Andreas; Stengel, Thomas; Litterst, Edwin; Kraut, Hans; Matuszczyk, Henry; Ailer, Franz; Hajkowski, Steve

2016-05-23

The representation of and search for generic chemical structures (Markush) remains a continuing challenge. Several research groups have addressed this problem, and over time a limited number of practical solutions have been proposed. Today there are two large commercial providers of Markush databases: Chemical Abstracts Service (CAS) and Thomson Reuters. The Thomson Reuters "Derwent" Markush database is currently offered via the online services Questel and STN and as a data feed for in-house use. The aim of this paper is to briefly review the existing Markush systems (databases plus search engines) and to describe our new approach for the implementation of the Derwent Markush Resource on STN. Our new approach demonstrates the integration of the Derwent Markush Resource database into the existing chemistry-focused STN platform without loss of detail. This provides compatibility with other structure and Markush databases on STN and at the same time makes it possible to deploy the specific features and functions of the Derwent approach. It is shown that the different Markush languages developed by CAS and Derwent can be combined into a single general Markush description. In this concept the generic nodes are grouped together in a unique hierarchy where all chemical elements and fragments can be integrated. As a consequence, both systems are searchable using a single structure query. Moreover, the presented concept could serve as a promising starting point for a common generalized description of Markush structures.

Intensity-modulated radiotherapy as primary treatment for prostate cancer: acute toxicity in 114 patients.

PubMed

De Meerleer, Gert; Vakaet, Luc; Meersschout, Sabine; Villeirs, Geert; Verbaeys, Antony; Oosterlinck, Wim; De Neve, Wilfried

2004-11-01

Dose escalation improves local control in prostate cancer. At Ghent University Hospital, intensity-modulated radiotherapy (IMRT) is used to increase the dose to the prostate and/or seminal vesicles. We report on acute toxicity in 114 patients who received IMRT for prostate cancer. Intensity-modulated radiotherapy was initiated after approval of our ethics committee. A class solution was used to plan all cases. Three beams (gantry 0 degrees , 116 degrees , and 244 degrees ) and anatomy-based segmentation were used to create an intensity-modulated dose distribution. Maximal rectal dose was set at 2 Gy per fraction. Detailed dose-volume histograms for all relevant structures were present. For all patients, we determined the pretreatment morbidity by a detailed preradiotherapy, in-house developed symptom scale. All patients were treated with 18 MV photons of an Elekta linear accelerator. Patients were seen on a weekly basis during treatment, and 1 month (M1) and 3 months (M3) thereafter. The registration of acute toxicity was standardized by a fixed questionnaire. The Radiation Therapy Oncology Group (RTOG) toxicity scale served as a basis, but additional symptoms, such as rectal blood loss, urgency, and incontinence, were scored as well. All 114 IMRT plans were delivered successfully without any interruption or technical problem. Daily treatment time was always less than 8 min and less than 6 min in 90% of the cases. Grade 1 and Grade 2 gastrointestinal (GI) toxicities were observed in 44% and 29% of the patients, respectively, during the whole period. If only the RTOG scale was used, Grade 1 and Grade 2 GI toxicities were noted in 39% and 27% of the patients, respectively, leaving 34% free of acute RTOG-scaled toxicity. Grade 3 genitourinary (GU) toxicity was seen in 8 patients (7%), all but 1 during treatment. Grade 2 and Grade 1 GU toxicities were seen in 36% and 47% of the patients, respectively, leaving only 10% free of acute GU toxicity. Anatomy-based IMRT to treat prostate cancer is incorporated into our daily routine without any problem. Acute toxicity is very low. Most of the recorded symptoms decrease over time, except for GI urgency and incontinence. The incorporation of additional symptoms makes the scoring more detailed.

A categorical structure-activity relationship analysis of the developmental toxicity of antithyroid drugs.

PubMed

Cunningham, Albert R; Carrasquer, C Alex; Mattison, Donald R

2009-01-01

The choice of therapeutic strategies for hyperthyroidism during pregnancy is limited. Surgery and radioiodine are typically avoided, leaving propylthiouracil and methimazole in the US. Carbimazole, a metabolic precursor of methimazole, is available in some countries outside of the US. In the US propylthiouracil is recommended because of concern about developmental toxicity from methimazole and carbimazole. Despite this recommendation, the data on developmental toxicity of all three agents are extremely limited and insufficient to support a policy given the broad use of methimazole and carbimazole around the world. In the absence of new human or animal data we describe the development of a new structure-activity relationship (SAR) model for developmental toxicity using the cat-SAR expert system. The SAR model was developed from data for 323 compounds evaluated for human developmental toxicity with 130 categorized as developmental toxicants and 193 as nontoxicants. Model cross-validation yielded a concordance between observed and predicted results between 79% to 81%. Based on this model, propylthiouracil, methimazole, and carbimazole were observed to share some structural features relating to human developmental toxicity. Thus given the need to treat women with Graves's disease during pregnancy, new molecules with minimized risk for developmental toxicity are needed. To help meet this challenge, the cat-SAR method would be a useful in screening new drug candidates for developmental toxicity as well as for investigating their mechanism of action.

Segue: A Spectroscopic Survey of 240,000 Stars With g = 14-20

DTIC Science & Technology

2009-05-01

24 Research School of Astronomy and Astrophysics, Australian National University, Weston, ACT 2611, Australia 25 Lawrence Berkeley National...main-sequence and evolved objects, with the goal of studying the kinematics and populations of our Galaxy and its halo. The spectra are clustered in 212...SEGUE Survey is the subject of this paper . The pro- cessed, searchable data archive from SEGUE was made publicly available in the Fall of 2008 as part

The Efficiency of Musical Emotions for the Reconciliation of Conceptual Dissonances

DTIC Science & Technology

2013-10-24

Final/Annual/Midterm Report for AOARD Grant 114103 "The efficiency of musical emotions for the reconciliation of conceptual...and will be added to a searchable DoD database. In the present project, PI developed theoretical foundation for the evolution of music in...which was experimentally created in 4-year-old children, who obeyed an experimenter’s warning not to play with a desired toy. Without exposure to music

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

Fox, G.C.; Stevens, P.R.; Rittenberg, A.

A compilation is presented of reaction data taken from experimental high energy physics journal articles, reports, preprints, theses, and other sources. Listings of all the data are given, and the data points are indexed by reaction and momentum, as well as by their source document. Much of the original compilation was done by others working in the field. The data presented also exist in the form of a computer-readable and searchable database; primitive access facilities for this database are available.

Distinct C9orf72-Associated Dipeptide Repeat Structures Correlate with Neuronal Toxicity

PubMed Central

Krans, Amy; Sawaya, Michael R.; Paulson, Henry L.; Todd, Peter K.; Barmada, Sami J.; Ivanova, Magdalena I.

2016-01-01

Hexanucleotide repeat expansions in C9orf72 are the most common inherited cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). The expansions elicit toxicity in part through repeat-associated non-AUG (RAN) translation of the intronic (GGGGCC)n sequence into dipeptide repeat-containing proteins (DPRs). Little is known, however, about the structural characteristics and aggregation propensities of the dipeptide units comprising DPRs. To address this question, we synthesized dipeptide units corresponding to the three sense-strand RAN translation products, analyzed their structures by circular dichroism, electron microscopy and dye binding assays, and assessed their relative toxicity when applied to primary cortical neurons. Short, glycine-arginine (GR)3 dipeptides formed spherical aggregates and selectively reduced neuronal survival compared to glycine-alanine (GA)3 and glycine-proline (GP)3 dipeptides. Doubling peptide length had little effect on the structure of GR or GP peptides, but (GA)6 peptides formed β-sheet rich aggregates that bound thioflavin T and Congo red yet lacked the typical fibrillar morphology of amyloids. Aging of (GA)6 dipeptides increased their β-sheet content and enhanced their toxicity when applied to neurons. We also observed that the relative toxicity of each tested dipeptide was proportional to peptide internalization. Our results demonstrate that different C9orf72-related dipeptides exhibit distinct structural properties that correlate with their relative toxicity. PMID:27776165

SAR STUDY OF NASAL TOXICITY: LESSONS FOR MODELING SMALL TOXICITY DATASETS

EPA Science Inventory

Most toxicity data, particularly from whole animal bioassays, are generated without the needs or capabilities of structure-activity relationship (SAR) modeling in mind. Some toxicity endpoints have been of sufficient regulatory concern to warrant large scale testing efforts (e.g....

Modeling late rectal toxicities based on a parameterized representation of the 3D dose distribution

NASA Astrophysics Data System (ADS)

Buettner, Florian; Gulliford, Sarah L.; Webb, Steve; Partridge, Mike

2011-04-01

Many models exist for predicting toxicities based on dose-volume histograms (DVHs) or dose-surface histograms (DSHs). This approach has several drawbacks as firstly the reduction of the dose distribution to a histogram results in the loss of spatial information and secondly the bins of the histograms are highly correlated with each other. Furthermore, some of the complex nonlinear models proposed in the past lack a direct physical interpretation and the ability to predict probabilities rather than binary outcomes. We propose a parameterized representation of the 3D distribution of the dose to the rectal wall which explicitly includes geometrical information in the form of the eccentricity of the dose distribution as well as its lateral and longitudinal extent. We use a nonlinear kernel-based probabilistic model to predict late rectal toxicity based on the parameterized dose distribution and assessed its predictive power using data from the MRC RT01 trial (ISCTRN 47772397). The endpoints under consideration were rectal bleeding, loose stools, and a global toxicity score. We extract simple rules identifying 3D dose patterns related to a specifically low risk of complication. Normal tissue complication probability (NTCP) models based on parameterized representations of geometrical and volumetric measures resulted in areas under the curve (AUCs) of 0.66, 0.63 and 0.67 for predicting rectal bleeding, loose stools and global toxicity, respectively. In comparison, NTCP models based on standard DVHs performed worse and resulted in AUCs of 0.59 for all three endpoints. In conclusion, we have presented low-dimensional, interpretable and nonlinear NTCP models based on the parameterized representation of the dose to the rectal wall. These models had a higher predictive power than models based on standard DVHs and their low dimensionality allowed for the identification of 3D dose patterns related to a low risk of complication.

Acute Oral Toxicity of Nitroguanidine in Male and Female Rats

DTIC Science & Technology

1988-03-01

results place nitroguanidlne in the practically nontoxic category based on the toxicity classification system of Hodge and Sterner. 20 DISTRIBUTION...nose and mouth. These results place nitroguanidine in the practically nontoxic category based on the toxicity classification system of Hodge and...O. Lollini, DVM, VC, Diplomate, American College of Veterinary Pathologists DATA MANAGERS: Carolyn M. Lewis, MS, Yvonne C. Le Tellier , BS REPORT

Testicular distribution and toxicity of a novel LTA4H inhibitor in rats

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

Ward, P.D., E-mail: pward4@its.jnj.com; La, D.

JNJ 40929837, a novel leukotriene A4 hydrolase inhibitor in drug development, was reported to induce testicular toxicity in rats. The mechanism of toxicity was considered to be rodent specific and not relevant to humans. To further investigate this finding in rats, the distribution and toxicokinetics of JNJ 40929837 and its two metabolites, M1 and M2, were investigated. A quantitative whole body autoradiography study showed preferential distribution and retention of JNJ 40929837-derived radioactivity in the testes consistent with the observed site of toxicity. Subsequent studies with unlabeled JNJ 40929837 showed different metabolite profiles between the plasma and testes. Following a singlemore » oral 50 mg/kg dose of JNJ 40929837, M2 was the primary metabolite in plasma whereas M1 was the primary metabolite in testes. The exposure of M1 was 386-fold higher in the testes compared to plasma whereas M2 had limited exposure in testes. Furthermore, the T{sub max} of M1 was 48 h in testes suggesting a large accumulation potential of this metabolite in testes compared to plasma. Following six months of repeated daily oral dosing, M1 accumulated approximately five-fold in the testes whereas the parent did not accumulate. These results indicate that the toxicokinetic profiles of JNJ 40929837 and its two metabolites in testes are markedly different compared to plasma and support the importance of understanding the toxicokinetic profiles of compounds and their metabolites in organs/tissues where toxicity is observed. - Highlights: • JNJ 40929837-derived radioactivity preferentially distributed into testes • Primary metabolite flip-flop in plasma and testes • The primary metabolite in testes accumulated 5-fold but not parent.« less

Comparative investigation of toxicity and bioaccumulation of Cd-based quantum dots and Cd salt in freshwater plant Lemna minor L.

PubMed

Modlitbová, Pavlína; Novotný, Karel; Pořízka, Pavel; Klus, Jakub; Lubal, Přemysl; Zlámalová-Gargošová, Helena; Kaiser, Jozef

2018-01-01

The purpose of this study was to determine the toxicity of two different sources of cadmium, i.e. CdCl 2 and Cd-based Quantum Dots (QDs), for freshwater model plant Lemna minor L. Cadmium telluride QDs were capped with two coating ligands: glutathione (GSH) or 3-mercaptopropionic acid (MPA). Growth rate inhibition and final biomass inhibition of L. minor after 168-h exposure were monitored as toxicity endpoints. Dose-response curves for Cd toxicity and EC50 168h values were statistically evaluated for all sources of Cd to uncover possible differences among the toxicities of tested compounds. Total Cd content and its bioaccumulation factors (BAFs) in L. minor after the exposure period were also determined to distinguish Cd bioaccumulation patterns with respect to different test compounds. Laser-Induced Breakdown Spectroscopy (LIBS) with lateral resolution of 200µm was employed in order to obtain two-dimensional maps of Cd spatial distribution in L. minor fronds. Our results show that GSH- and MPA-capped Cd-based QDs have similar toxicity for L. minor, but are significantly less toxic than CdCl 2 . However, both sources of Cd lead to similar patterns of Cd bioaccumulation and distribution in L. minor fronds. Our results are in line with previous reports that the main mediators of Cd toxicity and bioaccumulation in aquatic plants are Cd 2+ ions dissolved from Cd-based QDs. Copyright © 2017 Elsevier Inc. All rights reserved.

Maternally-Mediated Effects on Development*

EPA Science Inventory

In standard Segment II mammalian bioassays for developmental toxicity, it is the pregnant animal that is exposed to the test article, so in this sense, all in utero developmental toxicity is mediated by the mother. This will include absorption, distribution, metabolism and excret...

Development of oil product toxicity benchmarks using SSDs

EPA Science Inventory

Determining the sensitivity of a diversity of species to spilled oil and chemically dispersed oil continues to be a significant challenge in spill response and impact assessment. We developed species sensitivity distributions (SSDs) of acute toxicity values using standardized te...

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

deLorimier, Elaine; Coonrod, Leslie A.; Copperman, Jeremy

In this study, CUG repeat expansions in the 3' UTR of dystrophia myotonica protein kinase ( DMPK) cause myotonic dystrophy type 1 (DM1). As RNA, these repeats elicit toxicity by sequestering splicing proteins, such as MBNL1, into protein–RNA aggregates. Structural studies demonstrate that CUG repeats can form A-form helices, suggesting that repeat secondary structure could be important in pathogenicity. To evaluate this hypothesis, we utilized structure-stabilizing RNA modifications pseudouridine (Ψ) and 2'-O-methylation to determine if stabilization of CUG helical conformations affected toxicity. CUG repeats modified with Ψ or 2'-O-methyl groups exhibited enhanced structural stability and reduced affinity for MBNL1. Molecularmore » dynamics and X-ray crystallography suggest a potential water-bridging mechanism for Ψ-mediated CUG repeat stabilization. Ψ modification of CUG repeats rescued mis-splicing in a DM1 cell model and prevented CUG repeat toxicity in zebrafish embryos. This study indicates that the structure of toxic RNAs has a significant role in controlling the onset of neuromuscular diseases.« less

Manganese Transport and Toxicity in Polarized WIF-B Hepatocytes.

PubMed

Thompson, Khristy J; Hein, Jennifer; Baez, Andrew; Sosa, Jose Carlo; Wessling-Resnick, Marianne

2018-05-24

Mn toxicity arises from nutritional problems, community and occupational exposures, and genetic risks. Mn blood levels are controlled by hepatobiliary clearance. The goals of this study were to determine the cellular distribution of Mn transporters in polarized hepatocytes, to establish an in vitro assay for hepatocyte Mn efflux, and to examine possible roles the Mn transporters would play in metal import and export. For these experiments, hepatocytoma WIF-B cells were grown for 12-14 days to achieve maximal polarity. Immunoblots showed that Mn transporters ZIP8, ZnT10, ferroportin (Fpn), and ZIP14 were present. Indirect immunofluorescence microscopy localized Fpn and ZIP14 to WIF-B cell basolateral domains while ZnT10 and ZIP8 associated with intracellular vesicular compartments. ZIP8-positive structures were distributed uniformly throughout the cytoplasm, but ZnT10-positive vesicles were adjacent to apical bile compartments. WIF-B cells were sensitive to Mn toxicity, showing decreased viability after 16 h exposure to > 250 M MnCl2. However, the hepatocytes were resistant to 4 h exposures of up to 500 M MnCl2 despite 50-fold increased Mn content. Washout experiments showed time-dependent efflux with 80% Mn released after a 4 h chase period. Hepcidin reduced levels of Fpn in WIF-B cells, clearing Fpn from the cell surface, but Mn efflux was unaffected. The secretory inhibitor brefeldin A did block release of Mn from WIF-B cells, suggesting vesicle fusion may be involved in export. These results point to a possible role of ZnT10 to import Mn into vesicles that subsequently fuse with the apical membrane and empty their contents into bile.

Biogenic silver nanoparticles based on trichoderma harzianum: synthesis, characterization, toxicity evaluation and biological activity

NASA Astrophysics Data System (ADS)

Guilger, Mariana; Pasquoto-Stigliani, Tatiane; Bilesky-Jose, Natália; Grillo, Renato; Abhilash, P. C.; Fraceto, Leonardo Fernandes; Lima, Renata De

2017-03-01

White mold is an agricultural disease caused by the fungus Sclerotinia sclerotiorum, which affects important crops. There are different ways of controlling this organism, but none provides inhibition of its resistance structures (sclerotia). Nanotechnology offers promising applications in agricultural area. Here, silver nanoparticles were biogenically synthesized using the fungus Trichoderma harzianum and characterized. Cytotoxicity and genotoxicity were evaluated, and the nanoparticles were initially tested against white mold sclerotia. Their effects on soybean were also investigated with no effects observed. The nanoparticles showed potential against S. sclerotiorum, inhibiting sclerotia germination and mycelial growth. Nanoparticle characterization data indicated spherical morphology, satisfactory polydispersity and size distribution. Cytotoxicity and genotoxicity assays showed that the nanoparticles caused both the effects, although, the most toxic concentrations were above those applied for white mold control. Given the potential of the nanoparticles against S. sclerotiorum, we conclude that this study presents a first step for a new alternative in white mold control.

Computational Study on New Natural Compound Inhibitors of Pyruvate Dehydrogenase Kinases

PubMed Central

Zhou, Xiaoli; Yu, Shanshan; Su, Jing; Sun, Liankun

2016-01-01

Pyruvate dehydrogenase kinases (PDKs) are key enzymes in glucose metabolism, negatively regulating pyruvate dehyrogenase complex (PDC) activity through phosphorylation. Inhibiting PDKs could upregulate PDC activity and drive cells into more aerobic metabolism. Therefore, PDKs are potential targets for metabolism related diseases, such as cancers and diabetes. In this study, a series of computer-aided virtual screening techniques were utilized to discover potential inhibitors of PDKs. Structure-based screening using Libdock was carried out following by ADME (adsorption, distribution, metabolism, excretion) and toxicity prediction. Molecular docking was used to analyze the binding mechanism between these compounds and PDKs. Molecular dynamic simulation was utilized to confirm the stability of potential compound binding. From the computational results, two novel natural coumarins compounds (ZINC12296427 and ZINC12389251) from the ZINC database were found binding to PDKs with favorable interaction energy and predicted to be non-toxic. Our study provide valuable information of PDK-coumarins binding mechanisms in PDK inhibitor-based drug discovery. PMID:26959013

Computational Study on New Natural Compound Inhibitors of Pyruvate Dehydrogenase Kinases.

PubMed

Zhou, Xiaoli; Yu, Shanshan; Su, Jing; Sun, Liankun

2016-03-04

Pyruvate dehydrogenase kinases (PDKs) are key enzymes in glucose metabolism, negatively regulating pyruvate dehyrogenase complex (PDC) activity through phosphorylation. Inhibiting PDKs could upregulate PDC activity and drive cells into more aerobic metabolism. Therefore, PDKs are potential targets for metabolism related diseases, such as cancers and diabetes. In this study, a series of computer-aided virtual screening techniques were utilized to discover potential inhibitors of PDKs. Structure-based screening using Libdock was carried out following by ADME (adsorption, distribution, metabolism, excretion) and toxicity prediction. Molecular docking was used to analyze the binding mechanism between these compounds and PDKs. Molecular dynamic simulation was utilized to confirm the stability of potential compound binding. From the computational results, two novel natural coumarins compounds (ZINC12296427 and ZINC12389251) from the ZINC database were found binding to PDKs with favorable interaction energy and predicted to be non-toxic. Our study provide valuable information of PDK-coumarins binding mechanisms in PDK inhibitor-based drug discovery.

Assessing correlations between the spatial distribution of the dose to the rectal wall and late rectal toxicity after prostate radiotherapy: an analysis of data from the MRC RT01 trial (ISRCTN 47772397)

NASA Astrophysics Data System (ADS)

Buettner, Florian; Gulliford, Sarah L.; Webb, Steve; Sydes, Matthew R.; Dearnaley, David P.; Partridge, Mike

2009-11-01

Many studies have been performed to assess correlations between measures derived from dose-volume histograms and late rectal toxicities for radiotherapy of prostate cancer. The purpose of this study was to quantify correlations between measures describing the shape and location of the dose distribution and different outcomes. The dose to the rectal wall was projected on a two-dimensional map. In order to characterize the dose distribution, its centre of mass, longitudinal and lateral extent, and eccentricity were calculated at different dose levels. Furthermore, the dose-surface histogram (DSH) was determined. Correlations between these measures and seven clinically relevant rectal-toxicity endpoints were quantified by maximally selected standardized Wilcoxon rank statistics. The analysis was performed using data from the RT01 prostate radiotherapy trial. For some endpoints, the shape of the dose distribution is more strongly correlated with the outcome than simple DSHs. Rectal bleeding was most strongly correlated with the lateral extent of the dose distribution. For loose stools, the strongest correlations were found for longitudinal extent; proctitis was most strongly correlated with DSH. For the other endpoints no statistically significant correlations could be found. The strengths of the correlations between the shape of the dose distribution and outcome differed considerably between the different endpoints. Due to these significant correlations, it is desirable to use shape-based tools in order to assess the quality of a dose distribution.

Evaluation of in silico development of aquatic toxicity species sensitivity distributions

EPA Science Inventory

Determining the sensitivity of a diversity of species to environmental contaminants continues to be a significant challenge in ecological risk assessment because toxicity data are generally limited to a few standard test species. This study assessed whether species sensitivity d...

THE TOXICITY OF INDIUM

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

Downs, W.L.; Scott, J.K.; Steadman, L.T.

1959-09-16

Data are presented on the toxic effects of indium, administered as a chloride (InCl/sub 3/) or as an oxide (In/sub 2/O/sub 3/), in rats, rabbits, and dcgs. Data are included on the tissue distribution and excretion of indium-114. (C.H.)

SENSITIVITY DIFFERENCE AMONG VARIOUS STRAINS OF HYALLELA AZTECA

EPA Science Inventory

The North American amphipod Hyalella azteca is widely used in toxicity testing. H. azteca has a broad geographic distribution, and genetic evidence suggests that populations diverged from each other long ago. The importance of this genetic divergence to toxicity testing is uncle...

ACUTE TOXICITY OF PARA-NONYLPHENOL TO SALTWATER ANIMALS

EPA Science Inventory

?para-Nonylphenol (PNP), a mixture of alkylphenols used in producing nonionic surfactants, is distributed widely in surface waters and aquatic sediments, where it can affect saltwater species. This article describes a database for acute toxicity of PNP derived for calculating a n...

High-Resolution Chromosome Ideogram Representation of Currently Recognized Genes for Autism Spectrum Disorders

PubMed Central

Butler, Merlin G.; Rafi, Syed K.; Manzardo, Ann M.

2015-01-01

Recently, autism-related research has focused on the identification of various genes and disturbed pathways causing the genetically heterogeneous group of autism spectrum disorders (ASD). The list of autism-related genes has significantly increased due to better awareness with advances in genetic technology and expanding searchable genomic databases. We compiled a master list of known and clinically relevant autism spectrum disorder genes identified with supporting evidence from peer-reviewed medical literature sources by searching key words related to autism and genetics and from authoritative autism-related public access websites, such as the Simons Foundation Autism Research Institute autism genomic database dedicated to gene discovery and characterization. Our list consists of 792 genes arranged in alphabetical order in tabular form with gene symbols placed on high-resolution human chromosome ideograms, thereby enabling clinical and laboratory geneticists and genetic counsellors to access convenient visual images of the location and distribution of ASD genes. Meaningful correlations of the observed phenotype in patients with suspected/confirmed ASD gene(s) at the chromosome region or breakpoint band site can be made to inform diagnosis and gene-based personalized care and provide genetic counselling for families. PMID:25803107

Lunar e-Library: Putting Space History to Work

NASA Technical Reports Server (NTRS)

McMahan, Tracy A.; Shea, Charlotte A.; Finckenor, Miria

2006-01-01

As NASA plans and implements the Vision for Space Exploration, managers, engineers, and scientists need historically important information that is readily available and easily accessed. The Lunar e-Library - a searchable collection of 1100 electronic (.PDF) documents - makes it easy to find critical technical data and lessons learned and put space history knowledge in action. The Lunar e-Library, a DVD knowledge database, was developed by NASA to shorten research time and put knowledge at users' fingertips. Funded by NASA's Space Environments and Effects (SEE) Program headquartered at Marshall Space Flight Center (MSFC) and the MSFC Materials and Processes Laboratory, the goal of the Lunar e- Library effort was to identify key lessons learned from Apollo and other lunar programs and missions and to provide technical information from those programs in an easy-to-use format. The SEE Program began distributing the Lunar e-Library knowledge database in 2006. This paper describes the Lunar e-Library development process (including a description of the databases and resources used to acquire the documents) and the contents of the DVD product, demonstrates its usefulness with focused searches, and provides information on how to obtain this free resource.

From ontology selection and semantic web to an integrated information system for food-borne diseases and food safety.

PubMed

Yan, Xianghe; Peng, Yun; Meng, Jianghong; Ruzante, Juliana; Fratamico, Pina M; Huang, Lihan; Juneja, Vijay; Needleman, David S

2011-01-01

Several factors have hindered effective use of information and resources related to food safety due to inconsistency among semantically heterogeneous data resources, lack of knowledge on profiling of food-borne pathogens, and knowledge gaps among research communities, government risk assessors/managers, and end-users of the information. This paper discusses technical aspects in the establishment of a comprehensive food safety information system consisting of the following steps: (a) computational collection and compiling publicly available information, including published pathogen genomic, proteomic, and metabolomic data; (b) development of ontology libraries on food-borne pathogens and design automatic algorithms with formal inference and fuzzy and probabilistic reasoning to address the consistency and accuracy of distributed information resources (e.g., PulseNet, FoodNet, OutbreakNet, PubMed, NCBI, EMBL, and other online genetic databases and information); (c) integration of collected pathogen profiling data, Foodrisk.org ( http://www.foodrisk.org ), PMP, Combase, and other relevant information into a user-friendly, searchable, "homogeneous" information system available to scientists in academia, the food industry, and government agencies; and (d) development of a computational model in semantic web for greater adaptability and robustness.

Sulfur Mediated Alleviation of Mn Toxicity in Polish Wheat Relates to Regulating Mn Allocation and Improving Antioxidant System

PubMed Central

Sheng, Huajin; Zeng, Jian; Liu, Yang; Wang, Xiaolu; Wang, Yi; Kang, Houyang; Fan, Xing; Sha, Lina; Zhang, Haiqin; Zhou, Yonghong

2016-01-01

Sulfur (S) is an essential macronutrient that has been proved to play an important role in regulating plant responses to various biotic and abiotic stresses. The present study was designed to investigate the effect of S status on polish wheat plant response to Mn toxicity. Results showed that Mn stress inhibited plant growth, disturbed photosynthesis and induced oxidative stress. In response to Mn stress, polish wheat plant activated several detoxification mechanisms to counteract Mn toxicity, including enhanced antioxidant defense system, increased Mn distribution in the cell wall and up-regulated genes involved in S assimilation. Moderate S application was found to alleviate Mn toxicity mainly by sequestering excess Mn into vacuoles, inhibiting Mn translocation from roots to shoots, stimulating activities of antioxidant enzymes and enhancing GSH production via up-regulating genes involved in S metabolism. However, application of high level S to Mn-stressed plants did not significantly alleviated Mn toxicity likely due to osmotic stress. In conclusion, moderate S application is beneficial to polish wheat plant against Mn toxicity, S exerts its effects via stimulating the antioxidant defense system and regulating the translocation and subcellular distribution of Mn, in which processes GSH plays an indispensable role. PMID:27695467

MOAtox: A comprehensive mode of action and acute aquatic toxicity database for predictive model development (SETAC abstract)

EPA Science Inventory

The mode of toxic action (MOA) has been recognized as a key determinant of chemical toxicity and as an alternative to chemical class-based predictive toxicity modeling. However, the development of quantitative structure activity relationship (QSAR) and other models has been limit...

MOAtox: A Comprehensive Mode of Action and Acute Aquatic Toxicity Database for Predictive Model Development

EPA Science Inventory

tThe mode of toxic action (MOA) has been recognized as a key determinant of chemical toxicity andas an alternative to chemical class-based predictive toxicity modeling. However, the development ofquantitative structure activity relationship (QSAR) and other models has been limite...

Phase I Metabolic Stability and Electrophilic Reactivity of 2-Phenylaminophenylacetic Acid Derived Compounds.

PubMed

Pang, Yi Yun; Tan, Yee Min; Chan, Eric Chun Yong; Ho, Han Kiat

2016-07-18

Diclofenac and lumiracoxib are two highly analogous 2-phenylaminophenylacetic acid anti-inflammatory drugs exhibiting occasional dose-limiting hepatotoxicities. Prior data indicate that bioactivation and reactive metabolite formation play roles in the observed toxicity, but the exact chemical influence of the substituents remains elusive. In order to elucidate the role of chemical influence on metabolism related toxicity, metabolic stability and electrophilic reactivity were investigated for a series of structurally related analogues and their resulting metabolites. The resulting analogues embody progressive physiochemical changes through varying halogeno- and aliphatic substituents at two positions and were subjected to in vitro human liver microsomal metabolic stability and cell-based GSH depletion assays (to measure electrophilic reactivity). LC-MS/MS analysis of the GSH trapped reactive intermediates derived from the analogues was then used to identify the putative structures of reactive metabolites. We found that chemical modifications of the structural backbone led to noticeable perturbations of metabolic stability, electrophilic reactivity, and structures and composition of reactive metabolites. With the acquired data, the relationships between stability, reactivity, and toxicity were investigated in an attempt to correlate between Phase I metabolism and in vitro toxicity. A positive correlation was identified between reactivity and in vitro toxicity, indicating that electrophilic reactivity can be an indicator for in vitro toxicity. All in all, the effect of substituents on the structures and reactivity of the metabolites, however subtle the changes, should be taken into consideration during future drug design involving similar chemical features.

Common structural features of toxic intermediates from α-synuclein and GroES fibrillogenesis detected using cryogenic coherent X-ray diffraction imaging.

PubMed

Kameda, Hiroshi; Usugi, Sayaka; Kobayashi, Mana; Fukui, Naoya; Lee, Seki; Hongo, Kunihiro; Mizobata, Tomohiro; Sekiguchi, Yuki; Masaki, Yu; Kobayashi, Amane; Oroguchi, Tomotaka; Nakasako, Masayoshi; Takayama, Yuki; Yamamoto, Masaki; Kawata, Yasushi

2017-01-01

The aggregation and deposition of α-synuclein (αSyn) in neuronal cells is correlated to pathogenesis of Parkinson's disease. Although the mechanism of αSyn aggregation and fibril formation has been studied extensively, the structural hallmarks that are directly responsible for toxicity toward cells are still under debate. Here, we have compared the structural characteristics of the toxic intermediate molecular species of αSyn and similar toxic species of another protein, GroES, using coherent X-ray diffraction analysis. Using coherent X-ray free electron laser pulses of SACLA, we analysed αSyn and GroES fibril intermediate species and characterized various aggregate structures. Unlike previous studies where an annular oligomeric form of αSyn was identified, particle reconstruction from scattering traces suggested that the specific forms of the toxic particles were varied, with the sizes of the particles falling within a specific range. We did however discover a common structural feature in both αSyn and GroES samples; the edges of the detected particles were nearly parallel and produced a characteristic diffraction pattern in the diffraction experiments. The presence of parallel-edged particles in toxic intermediates of αSyn and GroES fibrillogenesis pointed towards a plausible common molecular interface that leads to the formation of mature fibrils. © The Authors 2016. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

Proposal of an in silico profiler for categorisation of repeat dose toxicity data of hair dyes.

PubMed

Nelms, M D; Ates, G; Madden, J C; Vinken, M; Cronin, M T D; Rogiers, V; Enoch, S J

2015-05-01

This study outlines the analysis of 94 chemicals with repeat dose toxicity data taken from Scientific Committee on Consumer Safety opinions for commonly used hair dyes in the European Union. Structural similarity was applied to group these chemicals into categories. Subsequent mechanistic analysis suggested that toxicity to mitochondria is potentially a key driver of repeat dose toxicity for chemicals within each of the categories. The mechanistic hypothesis allowed for an in silico profiler consisting of four mechanism-based structural alerts to be proposed. These structural alerts related to a number of important chemical classes such as quinones, anthraquinones, substituted nitrobenzenes and aromatic azos. This in silico profiler is intended for grouping chemicals into mechanism-based categories within the adverse outcome pathway paradigm.

Project management web tools at the MICE experiment

NASA Astrophysics Data System (ADS)

Coney, L. R.; Tunnell, C. D.

2012-12-01

Project management tools like Trac are commonly used within the open-source community to coordinate projects. The Muon Ionization Cooling Experiment (MICE) uses the project management web application Redmine to host mice.rl.ac.uk. Many groups within the experiment have a Redmine project: analysis, computing and software (including offline, online, controls and monitoring, and database subgroups), executive board, and operations. All of these groups use the website to communicate, track effort, develop schedules, and maintain documentation. The issue tracker is a rich tool that is used to identify tasks and monitor progress within groups on timescales ranging from immediate and unexpected problems to milestones that cover the life of the experiment. It allows the prioritization of tasks according to time-sensitivity, while providing a searchable record of work that has been done. This record of work can be used to measure both individual and overall group activity, identify areas lacking sufficient personnel or effort, and as a measure of progress against the schedule. Given that MICE, like many particle physics experiments, is an international community, such a system is required to allow easy communication within a global collaboration. Unlike systems that are purely wiki-based, the structure of a project management tool like Redmine allows information to be maintained in a more structured and logical fashion.

The Planetary Data System — Renewing Our Science Nodes in Order to Better Serve Our Science Community

NASA Astrophysics Data System (ADS)

Morgan, T. H.; McLaughlin, S.; Grayzeck, E. J.; Knopf, W.; McNutt, R. L., Jr.; Crichton, D. J.; New, M. H.

2015-12-01

In order to improve NASA's ability to provide an agile response to the needs of the Planetary Science Community, the Planetary Data System (PDS) is being transformed. NASA has used the highly successful virtual institute model (e.g., for NASA's Astrobiology Program) to re-compete the Science Nodes within the PDS Structure. We expect the new PDS will improve both archive searchability and product discoverability, continue the adaption of the new PDS4 Standard, and enhance our ability to work with other archive/curation activities within NASA and with the International community of space faring nations (through the International Planetary Data Alliance). PDS will continue to work with NASA missions from the initial Announcement of Opportunity through the end of mission to define, organize, and document the data. This process includes peer-review of data sets by members of the science community to ensure that the data sets are scientifically useful, effectively organized, and well documented. In this presentation we discuss recent changes in the PDS, and our future activities to build on these changes. Please visit our User Support Area at the meeting (Booth #446) if you have questions accessing our data sets or providing data to the PDS or about the new PDS structure.

PAMDB: a comprehensive Pseudomonas aeruginosa metabolome database.

PubMed

Huang, Weiliang; Brewer, Luke K; Jones, Jace W; Nguyen, Angela T; Marcu, Ana; Wishart, David S; Oglesby-Sherrouse, Amanda G; Kane, Maureen A; Wilks, Angela

2018-01-04

The Pseudomonas aeruginosaMetabolome Database (PAMDB, http://pseudomonas.umaryland.edu) is a searchable, richly annotated metabolite database specific to P. aeruginosa. P. aeruginosa is a soil organism and significant opportunistic pathogen that adapts to its environment through a versatile energy metabolism network. Furthermore, P. aeruginosa is a model organism for the study of biofilm formation, quorum sensing, and bioremediation processes, each of which are dependent on unique pathways and metabolites. The PAMDB is modelled on the Escherichia coli (ECMDB), yeast (YMDB) and human (HMDB) metabolome databases and contains >4370 metabolites and 938 pathways with links to over 1260 genes and proteins. The database information was compiled from electronic databases, journal articles and mass spectrometry (MS) metabolomic data obtained in our laboratories. For each metabolite entered, we provide detailed compound descriptions, names and synonyms, structural and physiochemical information, nuclear magnetic resonance (NMR) and MS spectra, enzymes and pathway information, as well as gene and protein sequences. The database allows extensive searching via chemical names, structure and molecular weight, together with gene, protein and pathway relationships. The PAMBD and its future iterations will provide a valuable resource to biologists, natural product chemists and clinicians in identifying active compounds, potential biomarkers and clinical diagnostics. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Department of Defense Dictionary of Military and Associated Terms

DTIC Science & Technology

2010-11-08

Terminology. 4. Publication Format This edition of JP 1-02 has been published in two basic parts: a . Terms and definitions. These are...understanding and management of the associated term. 5. JP 1-02 Online Availability and Update Schedule JP 1-02 is accessible online as a searchable...As Amended Through 15 February 2016 ii JP 1-02 address: https://jdeis.js.mil/jdeis/. The contents of JP 1-02 are updated on a monthly basis to

Redesign of Advanced Education Processes the United States Coast Guard

DTIC Science & Technology

1999-09-01

educational level. Els are assigned to help track individuals with specialized training and to facilitate statistical data collection. The El is used by...just like every other officer in the Coast Guard. Currently, the Coast Guard’s personnel database does not include data on advanced education ...Appendix A. 56 • Advanced Education is not a searchable field in the Coast Guard’s Personnel Data System. PMs and AOs do not have direct access to

ClinicalKey 2.0: Upgrades in a Point-of-Care Search Engine.

PubMed

Huslig, Mary Ann; Vardell, Emily

2015-01-01

ClinicalKey 2.0, launched September 23, 2014, offers a mobile-friendly design with a search history feature for targeting point-of-care resources for health care professionals. Browsing is improved with searchable, filterable listings of sources highlighting new resources. ClinicalKey 2.0 improvements include more than 1,400 new Topic Pages for quick access to point-of-care content. A sample search details some of the upgrades and content options.

Blind Seer: A Scalable Private DBMS

DTIC Science & Technology

2014-05-01

searchable index terms per DB row, in time comparable to (insecure) MySQL (many practical queries can be privately executed with work 1.2-3 times slower...than MySQL , although some queries are costlier). We support a rich query set, including searching on arbitrary boolean formulas on keywords and ranges...index terms per DB row, in time comparable to (insecure) MySQL (many practical queries can be privately executed with work 1.2-3 times slower than MySQL

Spectroscopic data for an astronomy database

NASA Technical Reports Server (NTRS)

Parkinson, W. H.; Smith, Peter L.

1995-01-01

Very few of the atomic and molecular data used in analyses of astronomical spectra are currently available in World Wide Web (WWW) databases that are searchable with hypertext browsers. We have begun to rectify this situation by making extensive atomic data files available with simple search procedures. We have also established links to other on-line atomic and molecular databases. All can be accessed from our database homepage with URL: http:// cfa-www.harvard.edu/ amp/ data/ amdata.html.

Energy Innovation Portal Brings DOE Technologies to the Market (Fact Sheet)

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

Not Available

2011-10-01

For venture capitalists, energy entrepreneurs, and industry veterans, finding the right renewable energy or energy efficiency solution used to be like looking for a needle in a haystack. Now, a searchable treasure trove of innovative U.S. Department of Energy (DOE) technologies is available. Created by the National Renewable Energy Laboratory (NREL), the online Energy Innovation Portal helps businesses and entrepreneurs access the intellectual property of DOE's 17 national laboratories and other research partners.

The use of high-throughput screening techniques to evaluate mitochondrial toxicity.

PubMed

Wills, Lauren P

2017-11-01

Toxicologists and chemical regulators depend on accurate and effective methods to evaluate and predict the toxicity of thousands of current and future compounds. Robust high-throughput screening (HTS) experiments have the potential to efficiently test large numbers of chemical compounds for effects on biological pathways. HTS assays can be utilized to examine chemical toxicity across multiple mechanisms of action, experimental models, concentrations, and lengths of exposure. Many agricultural, industrial, and pharmaceutical chemicals classified as harmful to human and environmental health exert their effects through the mechanism of mitochondrial toxicity. Mitochondrial toxicants are compounds that cause a decrease in the number of mitochondria within a cell, and/or decrease the ability of mitochondria to perform normal functions including producing adenosine triphosphate (ATP) and maintaining cellular homeostasis. Mitochondrial dysfunction can lead to apoptosis, necrosis, altered metabolism, muscle weakness, neurodegeneration, decreased organ function, and eventually disease or death of the whole organism. The development of HTS techniques to identify mitochondrial toxicants will provide extensive databases with essential connections between mechanistic mitochondrial toxicity and chemical structure. Computational and bioinformatics approaches can be used to evaluate compound databases for specific chemical structures associated with toxicity, with the goal of developing quantitative structure-activity relationship (QSAR) models and mitochondrial toxicophores. Ultimately these predictive models will facilitate the identification of mitochondrial liabilities in consumer products, industrial compounds, pharmaceuticals and environmental hazards. Copyright © 2017 Elsevier B.V. All rights reserved.

Exploring e-readers to support clinical medical education: two case studies*†

PubMed Central

von Isenburg, Megan

2011-01-01

Question: Can e-readers loaded with medical textbooks and other relevant material benefit medical students, residents, and preceptors in clinical settings? Settings: The settings are North Carolina community clinics served by Duke University Medical Center and St. Joseph's Hospital in Bryan, Texas, and Scott and White Memorial Hospital in Temple, Texas. Methods: Duke University: Twenty second-year medical students and fourteen family medicine clerkship preceptors used Kindle e-readers in clinics during eight months of rotations. Students and preceptors provided feedback through an anonymous online survey. Texas A&M University: Nine fourth-year medical students in an elective compared medical textbooks in print, online, and on a Kindle. Six residents at a local hospital completed an anonymous online survey after a three-week loan of a Kindle loaded with medical textbooks. Results: The e-reader's major advantages in clinical settings are portability and searchability. The selected e-reader's limitations include connection speed, navigation, and display. User preferences varied, but online resources were preferred. Participants suggested additional uses for Kindles in medical education. Conclusions: The selected e-reader's limitations may be resolved with further development of the device. Investigation of other e-readers is needed. Criteria for evaluating e-readers in clinical settings should include portability, searchability, speed, navigation, and display. Research comparing e-readers and mobile devices in clinical education is also warranted. PMID:21464848

DB-PABP: a database of polyanion-binding proteins

PubMed Central

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Russell Middaugh, C.

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references. PMID:17916573

DB-PABP: a database of polyanion-binding proteins.

PubMed

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Middaugh, C Russell

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

Comparative Toxicity of Selected Aviation Fuels as Measured by Insect Bioassay

DTIC Science & Technology

1982-07-01

structure in termites , ants, and bees can be used to contrast the toxicity of a compound. A comparative study of toxicity can also be made using a...and also serve as sex pheromones , kairomones, and defensive compounds. Cuticular hydrocarbons vary significantly in structure and amount by species...in flour beetles. Flour beetles contain hydrocarbons which function as sex pheromones and also contain a significant amount of 1-pentadecene which

MOLECULAR INTERACTION POTENTIALS FOR THE DEVELOPMENT OF STRUCTURE-ACTIVITY RELATIONSHIPS

EPA Science Inventory

Abstract
One reasonable approach to the analysis of the relationships between molecular structure and toxic activity is through the investigation of the forces and intermolecular interactions responsible for chemical toxicity. The interaction between the xenobiotic and the bio...

Impact of graphene-based nanomaterials (GBNMs) on the structural and functional conformations of hepcidin peptide

NASA Astrophysics Data System (ADS)

Singh, Krishna P.; Baweja, Lokesh; Wolkenhauer, Olaf; Rahman, Qamar; Gupta, Shailendra K.

2018-03-01

Graphene-based nanomaterials (GBNMs) are widely used in various industrial and biomedical applications. GBNMs of different compositions, size and shapes are being introduced without thorough toxicity evaluation due to the unavailability of regulatory guidelines. Computational toxicity prediction methods are used by regulatory bodies to quickly assess health hazards caused by newer materials. Due to increasing demand of GBNMs in various size and functional groups in industrial and consumer based applications, rapid and reliable computational toxicity assessment methods are urgently needed. In the present work, we investigate the impact of graphene and graphene oxide nanomaterials on the structural conformations of small hepcidin peptide and compare the materials for their structural and conformational changes. Our molecular dynamics simulation studies revealed conformational changes in hepcidin due to its interaction with GBMNs, which results in a loss of its functional properties. Our results indicate that hepcidin peptide undergo severe structural deformations when superimposed on the graphene sheet in comparison to graphene oxide sheet. These observations suggest that graphene is more toxic than a graphene oxide nanosheet of similar area. Overall, this study indicates that computational methods based on structural deformation, using molecular dynamics (MD) simulations, can be used for the early evaluation of toxicity potential of novel nanomaterials.

Ring structure modifications of phenylalanine 19 increase fibrillation kinetics and reduce toxicity of amyloid β (1-40).

PubMed

Korn, Alexander; Surendran, Dayana; Krueger, Martin; Maiti, Sudipta; Huster, Daniel

2018-05-24

We investigated the influence of the chemical structure of the phenylalanine side chain in position 19 of the 40 residue amyloid β peptide. Side chain modifications in this position yielded fibrils of essentially unaltered morphology, structure, and dynamics, but significantly increased fibrillation kinetics and diminished the toxicity of the peptides.

A novel bio-safe phase separation process for preparing open-pore biodegradable polycaprolactone microparticles.

PubMed

Salerno, Aurelio; Domingo, Concepción

2014-09-01

Open-pore biodegradable microparticles are object of considerable interest for biomedical applications, particularly as cell and drug delivery carriers in tissue engineering and health care treatments. Furthermore, the engineering of microparticles with well definite size distribution and pore architecture by bio-safe fabrication routes is crucial to avoid the use of toxic compounds potentially harmful to cells and biological tissues. To achieve this important issue, in the present study a straightforward and bio-safe approach for fabricating porous biodegradable microparticles with controlled morphological and structural features down to the nanometer scale is developed. In particular, ethyl lactate is used as a non-toxic solvent for polycaprolactone particles fabrication via a thermal induced phase separation technique. The used approach allows achieving open-pore particles with mean particle size in the 150-250 μm range and a 3.5-7.9 m(2)/g specific surface area. Finally, the combination of thermal induced phase separation and porogen leaching techniques is employed for the first time to obtain multi-scaled porous microparticles with large external and internal pore sizes and potential improved characteristics for cell culture and tissue engineering. Samples were characterized to assess their thermal properties, morphology and crystalline structure features and textural properties. Copyright © 2014 Elsevier B.V. All rights reserved.

Evaluation of in silico development of aquatic toxicity species sensitivity distributions (SSDs)

EPA Science Inventory

Determining the sensitivity of a diversity of species to environmental contaminants continues to be a significant challenge in ecological risk assessment because toxicity data are generally limited to a few standard test species. This study assessed whether species sensitivity di...

Vanadium distribution in rats and DNA cleavage by vanadyl complex: implication for vanadium toxicity and biological effects.

PubMed Central

Sakurai, H

1994-01-01

Vanadium ion is toxic to animals. However, vanadium is also an agent used for chemoprotection against cancers in animals. To understand both the toxic and beneficial effects we studied vanadium distribution in rats. Accumulation of vanadium in the liver nuclei of rats given low doses of compounds in the +4 or +5 oxidation state was greater than in the liver nuclei of rats given high doses of vanadium compounds or the vanadate (+5 oxidation state) compound. Vanadium was incorporated exclusively in the vanadyl (+4 oxidation state) form. We also investigated the reactions of vanadyl ion and found that incubation of DNA with vanadyl ion and hydrogen peroxide (H2O2) led to intense DNA cleavage. ESR spin trapping demonstrated that hydroxyl radicals are generated during the reactions of vanadyl ion and H2O2. Thus, we propose that the mechanism for vanadium-dependent toxicity and antineoplastic action is due to DNA cleavage by hydroxyl radicals generated in living systems. PMID:7843133

Practices in management of cancer treatment-related cardiovascular toxicity: A cardio-oncology survey.

PubMed

Jovenaux, Ludovic; Cautela, Jennifer; Resseguier, Noemie; Pibarot, Michele; Taouqi, Myriam; Orabona, Morgane; Pinto, Johan; Peyrol, Michael; Barraud, Jeremie; Laine, Marc; Bonello, Laurent; Paganelli, Franck; Barlesi, Fabrice; Thuny, Franck

2017-08-15

Cardiovascular toxicity has become a challenging issue during cancer therapy. Nonetheless, there is a lack of consensual guidelines for their management. We aimed to determine the current practices of oncologists regarding cardiovascular toxicity related to anthracyclines, trastuzumab and angiogenic inhibitors and to gather their opinions on the development of cardio-oncology programs. A cross-sectional declarative study was submitted to French oncologists in the form of an individual, structured questionnaire. A total of 303 oncologists responded to the survey. Ninety-nine percent of oncologists prescribed cardiotoxic therapies, including anthracyclines (83%), trastuzumab (51%) and other angiogenic inhibitors (64%). The method adopted for managing cardiovascular toxicity was based on guidelines from expert oncology societies for only 35% of oncologists. None was aware of recommendations from expert cardiology societies. Prescription of pre-, peri- and post-therapy cardiovascular assessment was inconsistent and significantly less frequent for all classes of angiogenic inhibitors than for anthracyclines and trastuzumab (P<0.0001). Relative to pre-therapy assessment, post-therapy assessment was prescribed significantly less often for all cancer therapies (P<0.0001). Attitudes regarding the onset of left ventricular dysfunction were much more inconsistent when angiogenic inhibitors were involved. Additionally, the management of hypertension and QT prolongation was also inconsistent. Finally, 88% of oncologists supported projects of cardio-oncology programs development. Practices of oncologists are disparate in the field of cardiovascular toxicity. This finding underlines the complexity of managing many different situations and the need for distribution of formal guidelines from oncology and cardiology expert societies. The development of personalized cardio-oncology programs seems essential. Copyright © 2017 Elsevier B.V. All rights reserved.

Interoperability Outlook in the Big Data Future

NASA Astrophysics Data System (ADS)

Kuo, K. S.; Ramachandran, R.

2015-12-01

The establishment of distributed active archive centers (DAACs) as data warehouses and the standardization of file format by NASA's Earth Observing System Data Information System (EOSDIS) had doubtlessly propelled interoperability of NASA Earth science data to unprecedented heights in the 1990s. However, we obviously still feel wanting two decades later. We believe the inadequate interoperability we experience is a result of the the current practice that data are first packaged into files before distribution and only the metadata of these files are cataloged into databases and become searchable. Data therefore cannot be efficiently filtered. Any extensive study thus requires downloading large volumes of data files to a local system for processing and analysis.The need to download data not only creates duplication and inefficiency but also further impedes interoperability, because the analysis has to be performed locally by individual researchers in individual institutions. Each institution or researcher often has its/his/her own preference in the choice of data management practice as well as programming languages. Analysis results (derived data) so produced are thus subject to the differences of these practices, which later form formidable barriers to interoperability. A number of Big Data technologies are currently being examined and tested to address Big Earth Data issues. These technologies share one common characteristics: exploiting compute and storage affinity to more efficiently analyze large volumes and great varieties of data. Distributed active "archive" centers are likely to evolve into distributed active "analysis" centers, which not only archive data but also provide analysis service right where the data reside. "Analysis" will become the more visible function of these centers. It is thus reasonable to expect interoperability to improve because analysis, in addition to data, becomes more centralized. Within a "distributed active analysis center" interoperability is almost guaranteed because data, analysis, and results all can be readily shared and reused. Effectively, with the establishment of "distributed active analysis centers", interoperation turns from a many-to-many problem into a less complicated few-to-few problem and becomes easier to solve.

A compilation of safety impact information for extractables associated with materials used in pharmaceutical packaging, delivery, administration, and manufacturing systems.

PubMed

Jenke, Dennis; Carlson, Tage

2014-01-01

Demonstrating suitability for intended use is necessary to register packaging, delivery/administration, or manufacturing systems for pharmaceutical products. During their use, such systems may interact with the pharmaceutical product, potentially adding extraneous entities to those products. These extraneous entities, termed leachables, have the potential to affect the product's performance and/or safety. To establish the potential safety impact, drug products and their packaging, delivery, or manufacturing systems are tested for leachables or extractables, respectively. This generally involves testing a sample (either the extract or the drug product) by a means that produces a test method response and then correlating the test method response with the identity and concentration of the entity causing the response. Oftentimes, analytical tests produce responses that cannot readily establish the associated entity's identity. Entities associated with un-interpretable responses are termed unknowns. Scientifically justifiable thresholds are used to establish those individual unknowns that represent an acceptable patient safety risk and thus which do not require further identification and, conversely, those unknowns whose potential safety impact require that they be identified. Such thresholds are typically based on the statistical analysis of datasets containing toxicological information for more or less relevant compounds. This article documents toxicological information for over 540 extractables identified in laboratory testing of polymeric materials used in pharmaceutical applications. Relevant toxicological endpoints, such as NOELs (no observed effects), NOAELs (no adverse effects), TDLOs (lowest published toxic dose), and others were collated for these extractables or their structurally similar surrogates and were systematically assessed to produce a risk index, which represents a daily intake value for life-long intravenous administration. This systematic approach uses four uncertainty factors, each assigned a factor of 10, which consider the quality and relevance of the data, differences in route of administration, non-human species to human extrapolations, and inter-individual variation among humans. In addition to the risk index values, all extractables and most of their surrogates were classified for structural safety alerts using Cramer rules and for mutagenicity alerts using an in silico approach (Benigni/Bossa rule base for mutagenicity via Toxtree). Lastly, in vitro mutagenicity data (Ames Salmonella typimurium and Mouse Lymphoma tests) were collected from available databases (Chemical Carcinogenesis Research Information and Carcinogenic Potency Database). The frequency distributions of the resulting data were established; in general risk index values were normally distributed around a band ranging from 5 to 20 mg/day. The risk index associated with 95% level of the cumulative distribution plot was approximately 0.1 mg/day. Thirteen extractables in the dataset had individual risk index values less than 0.1 mg/day, although four of these had additional risk indices, based on multiple different toxicological endpoints, above 0.1 mg/day. Additionally, approximately 50% of the extractables were classified in Cramer Class 1 (low risk of toxicity) and approximately 35% were in Cramer Class 3 (no basis to assume safety). Lastly, roughly 20% of the extractables triggered either an in vitro or in silico alert for mutagenicity. When Cramer classifications and the mutagenicity alerts were compared to the risk indices, extractables with safety alerts generally had lower risk index values, although the differences in the risk index data distributions, extractables with or without alerts, were small and subtle. Leachables from packaging systems, manufacturing systems, or delivery devices can accumulate in drug products and potentially affect the drug product. Although drug products can be analyzed for leachables (and material extracts can be analyzed for extractables), not all leachables or extractables can be fully identified. Safety thresholds can be used to establish whether the unidentified substances can be deemed to be safe or whether additional analytical efforts need to be made to secure the identities. These thresholds are typically based on the statistical analysis of datasets containing toxicological information for more or less relevant compounds. This article contains safety data for over 500 extractables that were identified in laboratory characterizations of polymers used in pharmaceutical applications. The safety data consists of structural toxicity classifications of the extractables as well as calculated risk indices, where the risk indices were obtained by subjecting toxicological safety data, such as NOELs (no observed effects), NOAELs (no adverse effects), TDLOs (lowest published toxic dose), and others to a systematic evaluation process using appropriate uncertainty factors. Thus the risk index values represent daily exposures for the lifetime intravenous administration of drugs. The frequency distributions of the risk indices and Cramer classifications were examined. The risk index values were normally distributed around a range of 5 to 20 mg/day, and the risk index associated with the 95% level of the cumulative frequency plot was 0.1 mg/day. Approximately 50% of the extractables were in Cramer Class 1 (low risk of toxicity) and approximately 35% were in Cramer Class 3 (high risk of toxicity). Approximately 20% of the extractables produced an in vitro or in silico mutagenicity alert. In general, the distribution of risk index values was not strongly correlated with the either extractables' Cramer classification or by mutagenicity alerts. However, extractables with either in vitro or in silico alerts were somewhat more likely to have low risk index values. © PDA, Inc. 2014.

UV-visible degradation of boscalid--structural characterization of photoproducts and potential toxicity using in silico tests.

PubMed

Lassalle, Yannick; Kinani, Aziz; Rifai, Ahmad; Souissi, Yasmine; Clavaguera, Carine; Bourcier, Sophie; Jaber, Farouk; Bouchonnet, Stéphane

2014-05-30

Boscalid is a carboximide fungicide mainly used for vineyard protection as well as for tomato, apple, blueberry and various ornamental cultivations. The structural elucidation of by-products arising from the UV-visible photodegradation of boscalid has been investigated by gas chromatography/multi-stage mass spectrometry (GC/MS(n) ) and liquid chromatography/tandem mass spectrometry (LC/MS/MS) couplings. The potential toxicities of transformation products were estimated by in silico calculations. Aqueous solutions of boscalid were irradiated up to 150 min in a self-made reactor equipped with a mercury lamp. Analyses were carried out using a gas chromatograph coupled with an ion trap mass spectrometer operated in both electron ionization (EI) and chemical ionization (CI) modes and a liquid chromatograph coupled with a quadrupole time-of-flight (Q-TOF) mass spectrometer operated in electrospray ionization (ESI) mode. Multiple-stage collision-induced dissociation (CID) experiments were performed to establish dissociation pathways of ions. The QSAR (Quantitative Structure-Activity Relationship) T.E.S.T. program allowed the estimation of the toxicities of the by-products. Eight photoproducts were investigated. Chemical structures were proposed not only on the interpretation of multi-stage CID experiments, but also on kinetics data. These structures led us to suggest photodegradation pathways. Three photoproducts were finally detected in Lebanon in a real sample of grape leaves for which routine analysis had led to the detection of boscalid at 4 mg kg(-1). With one exception, the structures proposed for the photoproducts on the basis of mass spectra interpretation have not been reported in previous studies. In silico toxicity predictions showed that two photoproducts are potentially more toxic than the parent compound considering oral rat LD50 while five photoproducts may induce mutagenic toxicity. With the exception of one compound, all photoproducts may potentially induce developmental toxicity. Copyright © 2014 John Wiley & Sons, Ltd.

Classification of baseline toxicants for QSAR predictions to replace fish acute toxicity studies.

PubMed

Nendza, Monika; Müller, Martin; Wenzel, Andrea

2017-03-22

Fish acute toxicity studies are required for environmental hazard and risk assessment of chemicals by national and international legislations such as REACH, the regulations of plant protection products and biocidal products, or the GHS (globally harmonised system) for classification and labelling of chemicals. Alternative methods like QSARs (quantitative structure-activity relationships) can replace many ecotoxicity tests. However, complete substitution of in vivo animal tests by in silico methods may not be realistic. For the so-called baseline toxicants, it is possible to predict the fish acute toxicity with sufficient accuracy from log K ow and, hence, valid QSARs can replace in vivo testing. In contrast, excess toxicants and chemicals not reliably classified as baseline toxicants require further in silico, in vitro or in vivo assessments. Thus, the critical task is to discriminate between baseline and excess toxicants. For fish acute toxicity, we derived a scheme based on structural alerts and physicochemical property thresholds to classify chemicals as either baseline toxicants (=predictable by QSARs) or as potential excess toxicants (=not predictable by baseline QSARs). The step-wise approach identifies baseline toxicants (true negatives) in a precautionary way to avoid false negative predictions. Therefore, a certain fraction of false positives can be tolerated, i.e. baseline toxicants without specific effects that may be tested instead of predicted. Application of the classification scheme to a new heterogeneous dataset for diverse fish species results in 40% baseline toxicants, 24% excess toxicants and 36% compounds not classified. Thus, we can conclude that replacing about half of the fish acute toxicity tests by QSAR predictions is realistic to be achieved in the short-term. The long-term goals are classification criteria also for further groups of toxicants and to replace as many in vivo fish acute toxicity tests as possible with valid QSAR predictions.

Correlation between structure, retention, property, and activity of biologically relevant 1,7-bis(aminoalkyl)diazachrysene derivatives.

PubMed

Šegan, Sandra; Trifković, Jelena; Verbić, Tatjana; Opsenica, Dejan; Zlatović, Mario; Burnett, James; Šolaja, Bogdan; Milojković-Opsenica, Dušanka

2013-01-01

The physicochemical properties, retention parameters (R(M)(0)), partition coefficients (logP(OW)), and pK(a) values for a series of thirteen 1,7-bis(aminoalkyl) diazachrysene (1,7-DAAC) derivatives were determined in order to reveal the characteristics responsible for their biological behavior. The investigated compounds inhibit three unrelated pathogens (the Botulinum neurotoxin serotype A light chain (BoNT/A LC), Plasmodium falciparum malaria, and Ebola filovirus) via three different mechanisms of action. To determine the most influential factors governing the retention and activities of the investigated diazachrysenes, R(M)(0), logP(OW), and biological activity values were correlated with 2D and 3D molecular descriptors, using a partial least squares regression. The resulting quantitative structure-retention (property) relationships indicate the importance of descriptors related to the hydrophobicity of the molecules (e.g., predicted partition coefficients and hydrophobic surface area). Quantitative structure-activity relationship models for describing biological activity against the BoNT/A LC and malarial strains also include overall compound polarity, electron density distribution, and proton donor/acceptor potential. Furthermore, models for Ebola filovirus inhibition are presented qualitatively to provide insights into parameters that may contribute to the compounds' antiviral activities. Overall, the models form the basis for selecting structural features that significantly affect the compound's absorption, distribution, metabolism, excretion, and toxicity profiles. Copyright © 2012 Elsevier B.V. All rights reserved.

Quantitative Structure--Activity Relationship Modeling of Rat Acute Toxicity by Oral Exposure

EPA Science Inventory

Background: Few Quantitative Structure-Activity Relationship (QSAR) studies have successfully modeled large, diverse rodent toxicity endpoints. Objective: In this study, a combinatorial QSAR approach has been employed for the creation of robust and predictive models of acute toxi...

Detoxification of aflatoxins on prospective approach: effect on structural, mechanical, and optical properties under pressures.

PubMed

Wei, Yong-Kai; Zhao, Xiao-Miao; Li, Meng-Meng; Yu, Jing-Xin; Gurudeeban, Selvaraj; Hu, Yan-Fei; Ji, Guang-Fu; Wei, Dong-Qing

2018-06-01

Aflatoxins are sequential of derivatives of coumarin and dihydrofuran with similar chemical structures and well-known carcinogenic agent. Many studies performed to detoxify aflatoxins, but the result is not ideal. Therefore, we studied structural, infrared spectrum, mechanical, and optical properties of these compounds in the aim of perspective physics. Mulliken charge distributions and infrared spectral analysis performed to understand the structural difference between the basic types of aflatoxins. In addition, the effect of pressure, different polarized, and incident directions on their structural changes was determined. It is found that AFB 1 is most stable structure among four basic types aflatoxins (AFB 1 , AFB 2 , AFG 1 , and AFG 2 ), and IR spectra are analyzed to exhibit the difference on structures of them. The mechanical properties of AFB 1 indicate that the structure of this toxin can be easily changed by pressure. The real [Formula: see text] and imaginary [Formula: see text] parts of the dielectric function, and the absorption coefficient [Formula: see text] and energy loss spectrum [Formula: see text] were also obtained under different polarized and incident directions. Furthermore, biological experiments needed to support the toxic level of AFB 1 using optical technologies.

Biosorption and toxicity responses to arsenite (As[III]) in Scenedesmus quadricauda.

PubMed

Zhang, Jianying; Ding, Tengda; Zhang, Chunlong

2013-08-01

Toxicity and biosorption responses to arsenite (As[III]) were examined in a 96-h exposure study using Scenedesmus quadricauda, one of the most popular green algae distributed in freshwaters in China. Results indicated that the pH-dependent distribution of two arsenite species (H2AsO3(-) and H3AsO3) played an important role in biosorption and toxicity. The undissociated H3AsO3 was more toxic than its monoanionic H2AsO3(-) through comparison of algal cell numbers, chlorophyll-a contents, and algal ultrastructural changes observed with transmission electron microscopy. An effective biosorption of 89.0mgg(-1) at 100mgL(-1) As[III] was found in the treatments with an initial pH of 9.3 and 25.2μgg(-1) at 0.03mgL(-1) As[III] at an initial pH of 8.2 as a result of the predominant species of H2AsO3(-) under the ambient pH and Eh conditions. Our results imply that S. quadricauda may provide a new means for the removal of toxic arsenite species present in contaminated surface water. Copyright © 2013 Elsevier Ltd. All rights reserved.

TOWARDS REFINED USE OF TOXICITY DATA IN STATISTICALLY BASED SAR MODELS FOR DEVELOPMENTAL TOXICITY.

EPA Science Inventory

In 2003, an International Life Sciences Institute (ILSI) Working Group examined the potential of statistically based structure-activity relationship (SAR) models for use in screening environmental contaminants for possible developmental toxicants.

Fish acute toxicity syndromes and their use in the QSAR approach to hazard assessment.

PubMed Central

McKim, J M; Bradbury, S P; Niemi, G J

1987-01-01

Implementation of the Toxic Substances Control Act of 1977 creates the need to reliably establish testing priorities because laboratory resources are limited and the number of industrial chemicals requiring evaluation is overwhelming. The use of quantitative structure activity relationship (QSAR) models as rapid and predictive screening tools to select more potentially hazardous chemicals for in-depth laboratory evaluation has been proposed. Further implementation and refinement of quantitative structure-toxicity relationships in aquatic toxicology and hazard assessment requires the development of a "mode-of-action" database. With such a database, a qualitative structure-activity relationship can be formulated to assign the proper mode of action, and respective QSAR, to a given chemical structure. In this review, the development of fish acute toxicity syndromes (FATS), which are toxic-response sets based on various behavioral and physiological-biochemical measurements, and their projected use in the mode-of-action database are outlined. Using behavioral parameters monitored in the fathead minnow during acute toxicity testing, FATS associated with acetylcholinesterase (AChE) inhibitors and narcotics could be reliably predicted. However, compounds classified as oxidative phosphorylation uncouplers or stimulants could not be resolved. Refinement of this approach by using respiratory-cardiovascular responses in the rainbow trout, enabled FATS associated with AChE inhibitors, convulsants, narcotics, respiratory blockers, respiratory membrane irritants, and uncouplers to be correctly predicted. PMID:3297660

Development of a category approach to predict the testicular toxicity of chemical substances structurally related to ethylene glycol methyl ether.

PubMed

Yamada, Takashi; Tanaka, Yushiro; Hasegawa, Ryuichi; Sakuratani, Yuki; Yamazoe, Yasushi; Ono, Atsushi; Hirose, Akihiko; Hayashi, Makoto

2014-12-01

We propose a category approach to assessing the testicular toxicity of chemicals with a similar structure to ethylene glycol methyl ether (EGME). Based on toxicity information for EGME and related chemicals and accompanied by adverse outcome pathway information on the testicular toxicity of EGME, this category was defined as chemicals that are metabolized to methoxy- or ethoxyacetic acid, a substance responsible for testicular toxicity. A Japanese chemical inventory was screened using the Hazard Evaluation Support System, which we have developed to support a category approach for predicting the repeated-dose toxicity of chemical substances. Quantitative metabolic information on the related chemicals was then considered, and seventeen chemicals were finally obtained from the inventory as a shortlist for the category. Available data in the literature shows that chemicals for which information is available on the metabolic formation of EGME, ethylene glycol ethyl ether, methoxy- or ethoxyacetic acid do in fact possess testicular toxicity, suggesting that testicular toxicity is a concern, due to metabolic activation, for the remaining chemicals. Our results clearly demonstrate practical utility of AOP-based category approach for predicting repeated-dose toxicity of chemicals. Copyright © 2014 Elsevier Inc. All rights reserved.

Collagen-Based Biomaterials for Wound Healing

PubMed Central

Chattopadhyay, Sayani; Raines, Ronald T.

2014-01-01

With its wide distribution in soft and hard connective tissues, collagen is the most abundant of animal proteins. In vitro, natural collagen can be formed into highly organized, three-dimensional scaffolds that are intrinsically biocompatible, biodegradable, non-toxic upon exogenous application, and endowed with high tensile strength. These attributes make collagen the material of choice for wound healing and tissue engineering applications. In this article, we review the structure and molecular interactions of collagen in vivo; the recent use of natural collagen in sponges, injectables, films and membranes, dressings, and skin grafts; and the on-going development of synthetic collagen mimetic peptides as pylons to anchor cytoactive agents in wound beds. PMID:24633807

The case for regime-based water quality standards

USGS Publications Warehouse

Poole, Geoffrey C.; Dunham, J.B.; Keenan, D.M.; Sauter, S.T.; McCullough, D.A.; Mebane, Christopher; Lockwood, Jeffrey C.; Essig, Don A.; Hicks, Mark P.; Sturdevant, Debra J.; Materna, E.J.; Spalding, M.; Risley, John; Deppman, Marianne

2004-01-01

Conventional water quality standards have been successful in reducing the concentration of toxic substances in US waters. However, conventional standards are based on simple thresholds and are therefore poorly structured to address human-caused imbalances in dynamic, natural water quality parameters, such as nutrients, sediment, and temperature. A more applicable type of water quality standarda??a a??regime standarda??a??would describe desirable distributions of conditions over space and time within a stream network. By mandating the protection and restoration of the aquatic ecosystem dynamics that are required to support beneficial uses in streams, well-designed regime standards would facilitate more effective strategies for management of natural water quality parameters.

CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

EPA Science Inventory

Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

20180312 - Structure-based QSAR Models to Predict Systemic Toxicity Points of Departure (SOT)

EPA Science Inventory

Human health risk assessment associated with environmental chemical exposure is limited by the tens of thousands of chemicals with little or no experimental in vivo toxicity data. Data gap filling techniques, such as quantitative structure activity relationship (QSAR) models base...

Micro-PIXE mapping of elemental distribution in arbuscular mycorrhizal roots of the grass, Cynodon dactylon, from gold and uranium mine tailings

NASA Astrophysics Data System (ADS)

Weiersbye, I. M.; Straker, C. J.; Przybylowicz, W. J.

1999-10-01

A combination of PIXE, proton back-scattering (BS) spectrometry and confocal laser scanning microscopy (CLSM) was used to determine in situ elemental concentrations in arbuscular mycorrhizal (AM) grass roots and AM fungal spores from gold and uranium mine tailings in South Africa. AM regions of roots were characterised by locally elevated P and vesicles were defined by distinctive transition metal and radionuclide distributions. Vesicles (AM structures responsible for nutrient storage), accumulated Mn, Cu, Ni and U, whereas Fe and Zn were present at lower levels than in host tissue. AM spores from mine tailings accumulated Ca, Cr, Fe, Ni, Cu, Br, Y, Th and U, but were deficient in P and K. The sequestration of excess metals and radionuclides in vesicles may limit metal availability, and thus toxicity, to the host.

Biodegradable gelatin-based nanospheres as pH-responsive drug delivery systems

NASA Astrophysics Data System (ADS)

Curcio, Manuela; Altimari, Ilaria; Spizzirri, Umile Gianfranco; Cirillo, Giuseppe; Vittorio, Orazio; Puoci, Francesco; Picci, Nevio; Iemma, Francesca

2013-04-01

Native gelatin, N, N'-ethylenebisacrylamide, and sodium methacrylate were inserted into a spherical crosslinked structure by a solvent-free emulsion polymerization method, in which sunflower seed oil containing different amounts of lecithin was selected as continuous phase. Nanogels were characterized by morphological analysis, particle size distribution, and determination of swelling degree. Different dimensional distributions (100-500 nm) and water affinities were obtained by varying the amount of surfactant in the polymerization feed. Nanogels were non-toxic on human bone marrow mesenchymal stromal cells and enzymatically stable in the gastric tract, with weight losses ranging from 58 to 20 % in pancreatin solution. Release profiles of diclofenac sodium salt from the nanogels were evaluated at different pH and found to depend on crosslinking degree and drug-polymer interactions; while in pancreatin solution, a complete release of the drug was observed. The release mechanism and the diffusional contribution were evaluated by semiempirical equations.

Atomic structure of a toxic, oligomeric segment of SOD1 linked to amyotrophic lateral sclerosis (ALS)

PubMed Central

Sangwan, Smriti; Zhao, Anni; Adams, Katrina L.; Jayson, Christina K.; Sawaya, Michael R.; Guenther, Elizabeth L.; Pan, Albert C.; Ngo, Jennifer; Moore, Destaye M.; Soriaga, Angela B.; Do, Thanh D.; Goldschmidt, Lukasz; Nelson, Rebecca; Bowers, Michael T.; Koehler, Carla M.; Shaw, David E.; Novitch, Bennett G.; Eisenberg, David S.

2017-01-01

Fibrils and oligomers are the aggregated protein agents of neuronal dysfunction in ALS diseases. Whereas we now know much about fibril architecture, atomic structures of disease-related oligomers have eluded determination. Here, we determine the corkscrew-like structure of a cytotoxic segment of superoxide dismutase 1 (SOD1) in its oligomeric state. Mutations that prevent formation of this structure eliminate cytotoxicity of the segment in isolation as well as cytotoxicity of the ALS-linked mutants of SOD1 in primary motor neurons and in a Danio rerio (zebrafish) model of ALS. Cytotoxicity assays suggest that toxicity is a property of soluble oligomers, and not large insoluble aggregates. Our work adds to evidence that the toxic oligomeric entities in protein aggregation diseases contain antiparallel, out-of-register β-sheet structures and identifies a target for structure-based therapeutics in ALS. PMID:28760994

Understanding Genetic Toxicity Through Data Mining: The ...

EPA Pesticide Factsheets

This paper demonstrates the usefulness of representing a chemical by its structural features and the use of these features to profile a battery of tests rather than relying on a single toxicity test of a given chemical. This paper presents data mining/profiling methods applied in a weight-of-evidence approach to assess potential for genetic toxicity, and to guide the development of intelligent testing strategies. This paper demonstrates the usefulness of representing a chemical by its structural features and the use of these features to profile a battery of tests rather than relying on a single toxicity test of a given chemical. This paper presents data mining/profiling methods applied in a weight-of-evidence approach to assess potential for genetic toxicity, and to guide the development of intelligent testing strategies.

Biotic and abiotic studies on the biological fate, transport and ecotoxicity of toxic and hazardous waste in the Mississippi River basin

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

Abdelghani, A.; Pramar, Y.; Mandal, T.

1996-05-02

This project assesses the levels of xenobiotics in Devils Swamp and studies their biological fate, transport, ecotoxicity, and potential toxicity to man. This article reports on the following studies: assessment of the acute toxicity of individual xenobiotics and toxicity of organic compounds hexachlorobutadience (HCB) and hexachlorobenzene (HCBD) on juvenile crayfish; determination of the biotic influence of temperature, salinity, pH, oxidation-reduction potential, and sediment composition on the migration of xenobiotics; development of a pharmacokinetics model for xenobiotic absorption and storage, distribution and excretion by fish and crayfish.

TISSUE DISTRIBUTION OF ARSENIC SPECIES IN MICE CHRONICALLY EXPOSED TO METHYLARSONOUS ACID

EPA Science Inventory

The metabolism of inorganic arsenic (iAs) in humans yields toxic and carcinogenic methyl-As (MAs) and dimethyl-As (DMAs) intermediates. Methylarsonous acid (MAsIII) is the most acutely toxic species of characterized iAs metabolites. Here, we examined the concentrations of As spec...

Strike Up the Score: Deriving Searchable and Playable Digital Formats from Sheet Music; Smart Objects and Open Archives; Building the Archives of the Future: Advanced in Preserving Electronic Records at the National Archives and Records Administration; From the Digitized to the Digital Library.

ERIC Educational Resources Information Center

Choudhury, G. Sayeed; DiLauro, Tim; Droettboom, Michael; Fujinaga, Ichiro; MacMillan, Karl; Nelson, Michael L.; Maly, Kurt; Thibodeau, Kenneth; Thaller, Manfred

2001-01-01

These articles describe the experiences of the Johns Hopkins University library in digitizing their collection of sheet music; motivation for buckets, Smart Object, Dumb Archive (SODA) and the Open Archives Initiative (OAI), and initial experiences using them in digital library (DL) testbeds; requirements for archival institutions, the National…

Users’ guide to the surgical literature: how to perform a high-quality literature search

PubMed Central

Waltho, Daniel; Kaur, Manraj Nirmal; Haynes, R. Brian; Farrokhyar, Forough; Thoma, Achilleas

2015-01-01

Summary The article “Users’ guide to the surgical literature: how to perform a literature search” was published in 2003, but the continuing technological developments in databases and search filters have rendered that guide out of date. The present guide fills an existing gap in this area; it provides the reader with strategies for developing a searchable clinical question, creating an efficient search strategy, accessing appropriate databases, and skillfully retrieving the best evidence to address the research question. PMID:26384150

Systematic identification and analysis of frequent gene fusion events in metabolic pathways

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

Henry, Christopher S.; Lerma-Ortiz, Claudia; Gerdes, Svetlana Y.

Here, gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. As a result, here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These setsmore » were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. In conclusion, customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function.« less

Systematic identification and analysis of frequent gene fusion events in metabolic pathways

DOE PAGES

Henry, Christopher S.; Lerma-Ortiz, Claudia; Gerdes, Svetlana Y.; ...

2016-06-24

Here, gene fusions are the most powerful type of in silico-derived functional associations. However, many fusion compilations were made when <100 genomes were available, and algorithms for identifying fusions need updating to handle the current avalanche of sequenced genomes. The availability of a large fusion dataset would help probe functional associations and enable systematic analysis of where and why fusion events occur. As a result, here we present a systematic analysis of fusions in prokaryotes. We manually generated two training sets: (i) 121 fusions in the model organism Escherichia coli; (ii) 131 fusions found in B vitamin metabolism. These setsmore » were used to develop a fusion prediction algorithm that captured the training set fusions with only 7 % false negatives and 50 % false positives, a substantial improvement over existing approaches. This algorithm was then applied to identify 3.8 million potential fusions across 11,473 genomes. The results of the analysis are available in a searchable database. A functional analysis identified 3,000 reactions associated with frequent fusion events and revealed areas of metabolism where fusions are particularly prevalent. In conclusion, customary definitions of fusions were shown to be ambiguous, and a stricter one was proposed. Exploring the genes participating in fusion events showed that they most commonly encode transporters, regulators, and metabolic enzymes. The major rationales for fusions between metabolic genes appear to be overcoming pathway bottlenecks, avoiding toxicity, controlling competing pathways, and facilitating expression and assembly of protein complexes. Finally, our fusion dataset provides powerful clues to decipher the biological activities of domains of unknown function.« less

Cell-free protein synthesis for structure determination by X-ray crystallography.

PubMed

Watanabe, Miki; Miyazono, Ken-ichi; Tanokura, Masaru; Sawasaki, Tatsuya; Endo, Yaeta; Kobayashi, Ichizo

2010-01-01

Structure determination has been difficult for those proteins that are toxic to the cells and cannot be prepared in a large amount in vivo. These proteins, even when biologically very interesting, tend to be left uncharacterized in the structural genomics projects. Their cell-free synthesis can bypass the toxicity problem. Among the various cell-free systems, the wheat-germ-based system is of special interest due to the following points: (1) Because the gene is placed under a plant translational signal, its toxic expression in a bacterial host is reduced. (2) It has only little codon preference and, especially, little discrimination between methionine and selenomethionine (SeMet), which allows easy preparation of selenomethionylated proteins for crystal structure determination by SAD and MAD methods. (3) Translation is uncoupled from transcription, so that the toxicity of the translation product on DNA and its transcription, if any, can be bypassed. We have shown that the wheat-germ-based cell-free protein synthesis is useful for X-ray crystallography of one of the 4-bp cutter restriction enzymes, which are expected to be very toxic to all forms of cells retaining the genome. Our report on its structure represents the first report of structure determination by X-ray crystallography using protein overexpressed with the wheat-germ-based cell-free protein expression system. This will be a method of choice for cytotoxic proteins when its cost is not a problem. Its use will become popular when the crystal structure determination technology has evolved to require only a tiny amount of protein.