ECHO Services: Foundational Middleware for a Science Cyberinfrastructure

NASA Technical Reports Server (NTRS)

Burnett, Michael

2005-01-01

This viewgraph presentation describes ECHO, an interoperability middleware solution. It uses open, XML-based APIs, and supports net-centric architectures and solutions. ECHO has a set of interoperable registries for both data (metadata) and services, and provides user accounts and a common infrastructure for the registries. It is built upon a layered architecture with extensible infrastructure for supporting community unique protocols. It has been operational since November, 2002 and it available as open source.

Reducing costs of managing and accessing navigation and ancillary data by relying on the extensive capabilities of NASA's spice system

NASA Technical Reports Server (NTRS)

Semenov, Boris V.; Acton, Charles H., Jr.; Bachman, Nathaniel J.; Elson, Lee S.; Wright, Edward D.

2005-01-01

The SPICE system of navigation and ancillary data possesses a number of traits that make its use in modern space missions of all types highly cost efficient. The core of the system is a software library providing API interfaces for storing and retrieving such data as trajectories, orientations, time conversions, and instrument geometry parameters. Applications used at any stage of a mission life cycle can call SPICE APIs to access this data and compute geometric quantities required for observation planning, engineering assessment and science data analysis. SPICE is implemented in three different languages, supported on 20+ computer environments, and distributed with complete source code and documentation. It includes capabilities that are extensively tested by everyday use in many active projects and are applicable to all types of space missions - flyby, orbiters, observatories, landers and rovers. While a customer's initial SPICE adaptation for the first mission or experiment requires a modest effort, this initial effort pays off because adaptation for subsequent missions/experiments is just a small fraction of the initial investment, with the majority of tools based on SPICE requiring no or very minor changes.

A Driving Cycle Detection Approach Using Map Service API

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

Zhu, Lei; Gonder, Jeffrey D

Following advancements in smartphone and portable global positioning system (GPS) data collection, wearable GPS data have realized extensive use in transportation surveys and studies. The task of detecting driving cycles (driving or car-mode trajectory segments) from wearable GPS data has been the subject of much research. Specifically, distinguishing driving cycles from other motorized trips (such as taking a bus) is the main research problem in this paper. Many mode detection methods only focus on raw GPS speed data while some studies apply additional information, such as geographic information system (GIS) data, to obtain better detection performance. Procuring and maintaining dedicatedmore » road GIS data are costly and not trivial, whereas the technical maturity and broad use of map service application program interface (API) queries offers opportunities for mode detection tasks. The proposed driving cycle detection method takes advantage of map service APIs to obtain high-quality car-mode API route information and uses a trajectory segmentation algorithm to find the best-matched API route. The car-mode API route data combined with the actual route information, including the actual mode information, are used to train a logistic regression machine learning model, which estimates car modes and non-car modes with probability rates. The experimental results show promise for the proposed method's ability to detect vehicle mode accurately.« less

API REST Web service and backend system Of Lecturer’s Assessment Information System on Politeknik Negeri Bali

NASA Astrophysics Data System (ADS)

Manuaba, I. B. P.; Rudiastini, E.

2018-01-01

Assessment of lecturers is a tool used to measure lecturer performance. Lecturer’s assessment variable can be measured from three aspects : teaching activities, research and community service. Broad aspect to measure the performance of lecturers requires a special framework, so that the system can be developed in a sustainable manner. Issues of this research is to create a API web service data tool, so the lecturer assessment system can be developed in various frameworks. The research was developed with web service and php programming language with the output of json extension data. The conclusion of this research is API web service data application can be developed using several platforms such as web, mobile application

Engineering and algorithm design for an image processing Api: a technical report on ITK--the Insight Toolkit.

PubMed

Yoo, Terry S; Ackerman, Michael J; Lorensen, William E; Schroeder, Will; Chalana, Vikram; Aylward, Stephen; Metaxas, Dimitris; Whitaker, Ross

2002-01-01

We present the detailed planning and execution of the Insight Toolkit (ITK), an application programmers interface (API) for the segmentation and registration of medical image data. This public resource has been developed through the NLM Visible Human Project, and is in beta test as an open-source software offering under cost-free licensing. The toolkit concentrates on 3D medical data segmentation and registration algorithms, multimodal and multiresolution capabilities, and portable platform independent support for Windows, Linux/Unix systems. This toolkit was built using current practices in software engineering. Specifically, we embraced the concept of generic programming during the development of these tools, working extensively with C++ templates and the freedom and flexibility they allow. Software development tools for distributed consortium-based code development have been created and are also publicly available. We discuss our assumptions, design decisions, and some lessons learned.

Cyclone: java-based querying and computing with Pathway/Genome databases.

PubMed

Le Fèvre, François; Smidtas, Serge; Schächter, Vincent

2007-05-15

Cyclone aims at facilitating the use of BioCyc, a collection of Pathway/Genome Databases (PGDBs). Cyclone provides a fully extensible Java Object API to analyze and visualize these data. Cyclone can read and write PGDBs, and can write its own data in the CycloneML format. This format is automatically generated from the BioCyc ontology by Cyclone itself, ensuring continued compatibility. Cyclone objects can also be stored in a relational database CycloneDB. Queries can be written in SQL, and in an intuitive and concise object-oriented query language, Hibernate Query Language (HQL). In addition, Cyclone interfaces easily with Java software including the Eclipse IDE for HQL edition, the Jung API for graph algorithms or Cytoscape for graph visualization. Cyclone is freely available under an open source license at: http://sourceforge.net/projects/nemo-cyclone. For download and installation instructions, tutorials, use cases and examples, see http://nemo-cyclone.sourceforge.net.

Software Model Checking of ARINC-653 Flight Code with MCP

NASA Technical Reports Server (NTRS)

Thompson, Sarah J.; Brat, Guillaume; Venet, Arnaud

2010-01-01

The ARINC-653 standard defines a common interface for Integrated Modular Avionics (IMA) code. In particular, ARINC-653 Part 1 specifies a process- and partition-management API that is analogous to POSIX threads, but with certain extensions and restrictions intended to support the implementation of high reliability flight code. MCP is a software model checker, developed at NASA Ames, that provides capabilities for model checking C and C++ source code. In this paper, we present recent work aimed at implementing extensions to MCP that support ARINC-653, and we discuss the challenges and opportunities that consequentially arise. Providing support for ARINC-653 s time and space partitioning is nontrivial, though there are implicit benefits for partial order reduction possible as a consequence of the API s strict interprocess communication policy.

Using Map Service API for Driving Cycle Detection for Wearable GPS Data: Preprint

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

Zhu, Lei; Gonder, Jeffrey D

Following advancements in smartphone and portable global positioning system (GPS) data collection, wearable GPS data have realized extensive use in transportation surveys and studies. The task of detecting driving cycles (driving or car-mode trajectory segments) from wearable GPS data has been the subject of much research. Specifically, distinguishing driving cycles from other motorized trips (such as taking a bus) is the main research problem in this paper. Many mode detection methods only focus on raw GPS speed data while some studies apply additional information, such as geographic information system (GIS) data, to obtain better detection performance. Procuring and maintaining dedicatedmore » road GIS data are costly and not trivial, whereas the technical maturity and broad use of map service application program interface (API) queries offers opportunities for mode detection tasks. The proposed driving cycle detection method takes advantage of map service APIs to obtain high-quality car-mode API route information and uses a trajectory segmentation algorithm to find the best-matched API route. The car-mode API route data combined with the actual route information, including the actual mode information, are used to train a logistic regression machine learning model, which estimates car modes and non-car modes with probability rates. The experimental results show promise for the proposed method's ability to detect vehicle mode accurately.« less

A Shellcode Detection Method Based on Full Native API Sequence and Support Vector Machine

NASA Astrophysics Data System (ADS)

Cheng, Yixuan; Fan, Wenqing; Huang, Wei; An, Jing

2017-09-01

Dynamic monitoring the behavior of a program is widely used to discriminate between benign program and malware. It is usually based on the dynamic characteristics of a program, such as API call sequence or API call frequency to judge. The key innovation of this paper is to consider the full Native API sequence and use the support vector machine to detect the shellcode. We also use the Markov chain to extract and digitize Native API sequence features. Our experimental results show that the method proposed in this paper has high accuracy and low detection rate.

Comparison of plasma amino acid profile-based index and CA125 in the diagnosis of epithelial ovarian cancers and borderline malignant tumors.

PubMed

Miyagi, Etsuko; Maruyama, Yasuyo; Mogami, Tae; Numazaki, Reiko; Ikeda, Atsuko; Yamamoto, Hiroshi; Hirahara, Fumiki

2017-02-01

We previously developed a new plasma amino acid profile-based index (API) to detect ovarian, cervical, and endometrial cancers. Here, we compared API to serum cancer antigen 125 (CA125) for distinguishing epithelial ovarian malignant tumors from benign growths. API and CA125 were measured preoperatively in patients with ovarian tumors, which were later classified into 59 epithelial ovarian cancers, 21 epithelial borderline malignant tumors, and 97 benign tumors including 40 endometriotic cysts. The diagnostic accuracy and cutoff points of API were evaluated using receiver operating characteristic (ROC) curves. The area under the ROC curves showed the equivalent performance of API and CA125 to discriminate between malignant/borderline malignant and benign tumors (both 0.77), and API was superior to CA125 for discrimination between malignant/borderline malignant lesions and endometriotic cysts (API, 0.75 vs. CA125, 0.59; p < 0.05). At the API cutoff level of 6.0, API and CA125 had equal positive rates of detecting cancers and borderline malignancies (API, 0.71 vs. CA125, 0.74; p = 0.84) or cancers alone (API, 0.73 vs. CA125, 0.85; p = 0.12). However, API had a significantly lower detection rate of benign endometriotic cysts (0.35; 95 % CI, 0.21-0.52) compared with that of CA125 (0.65; 95 % CI, 0.48-0.79) (p < 0.05). API is an effective new tumor marker to detect ovarian cancers and borderline malignancies with a low false-positive rate for endometriosis. A large-scale prospective clinical study using the cutoff value of API determined in this study is warranted to validate API for practical clinical use.

Towards Standardized Patient Data Exchange: Integrating a FHIR Based API for the Open Medical Record System.

PubMed

Kasthurirathne, Suranga N; Mamlin, Burke; Grieve, Grahame; Biondich, Paul

2015-01-01

Interoperability is essential to address limitations caused by the ad hoc implementation of clinical information systems and the distributed nature of modern medical care. The HL7 V2 and V3 standards have played a significant role in ensuring interoperability for healthcare. FHIR is a next generation standard created to address fundamental limitations in HL7 V2 and V3. FHIR is particularly relevant to OpenMRS, an Open Source Medical Record System widely used across emerging economies. FHIR has the potential to allow OpenMRS to move away from a bespoke, application specific API to a standards based API. We describe efforts to design and implement a FHIR based API for the OpenMRS platform. Lessons learned from this effort were used to define long term plans to transition from the legacy OpenMRS API to a FHIR based API that greatly reduces the learning curve for developers and helps enhance adhernce to standards.

The tissue microarray data exchange specification: A document type definition to validate and enhance XML data

PubMed Central

Nohle, David G; Ayers, Leona W

2005-01-01

Background The Association for Pathology Informatics (API) Extensible Mark-up Language (XML) TMA Data Exchange Specification (TMA DES) proposed in April 2003 provides a community-based, open source tool for sharing tissue microarray (TMA) data in a common format. Each tissue core within an array has separate data including digital images; therefore an organized, common approach to produce, navigate and publish such data facilitates viewing, sharing and merging TMA data from different laboratories. The AIDS and Cancer Specimen Resource (ACSR) is a HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers HIV-related malignancies and uninfected control tissues in microarrays (TMA) accompanied by de-identified clinical data to approved researchers. Exporting our TMA data into the proposed API specified format offers an opportunity to evaluate the API specification in an applied setting and to explore its usefulness. Results A document type definition (DTD) that governs the allowed common data elements (CDE) in TMA DES export XML files was written, tested and evolved and is in routine use by the ACSR. This DTD defines TMA DES CDEs which are implemented in an external file that can be supplemented by internal DTD extensions for locally defined TMA data elements (LDE). Conclusion ACSR implementation of the TMA DES demonstrated the utility of the specification and allowed application of a DTD to validate the language of the API specified XML elements and to identify possible enhancements within our TMA data management application. Improvements to the specification have additionally been suggested by our experience in importing other institution's exported TMA data. Enhancements to TMA DES to remove ambiguous situations and clarify the data should be considered. Better specified identifiers and hierarchical relationships will make automatic use of the data possible. Our tool can be used to reorder data and add identifiers; upgrading data for changes in the specification can be automatically accomplished. Using a DTD (optionally reflecting our proposed enhancements) can provide stronger validation of exported TMA data. PMID:15871741

Correlation analysis of air pollutant index levels and dengue cases across five different zones in Selangor, Malaysia.

PubMed

Thiruchelvam, Loshini; Dass, Sarat C; Zaki, Rafdzah; Yahya, Abqariyah; Asirvadam, Vijanth S

2018-05-07

This study investigated the potential relationship between dengue cases and air quality - as measured by the Air Pollution Index (API) for five zones in the state of Selangor, Malaysia. Dengue case patterns can be learned using prediction models based on feedback (lagged terms). However, the question whether air quality affects dengue cases is still not thoroughly investigated based on such feedback models. This work developed dengue prediction models using the autoregressive integrated moving average (ARIMA) and ARIMA with an exogeneous variable (ARIMAX) time series methodologies with API as the exogeneous variable. The Box Jenkins approach based on maximum likelihood was used for analysis as it gives effective model estimates and prediction. Three stages of model comparison were carried out for each zone: first with ARIMA models without API, then ARIMAX models with API data from the API station for that zone and finally, ARIMAX models with API data from the zone and spatially neighbouring zones. Bayesian Information Criterion (BIC) gives goodness-of-fit versus parsimony comparisons between all elicited models. Our study found that ARIMA models, with the lowest BIC value, outperformed the rest in all five zones. The BIC values for the zone of Kuala Selangor were -800.66, -796.22, and -790.5229, respectively, for ARIMA only, ARIMAX with single API component and ARIMAX with API components from its zone and spatially neighbouring zones. Therefore, we concluded that API levels, either temporally for each zone or spatio- temporally based on neighbouring zones, do not have a significant effect on dengue cases.

Gas chromatography coupled to atmospheric pressure ionization mass spectrometry (GC-API-MS): review.

PubMed

Li, Du-Xin; Gan, Lin; Bronja, Amela; Schmitz, Oliver J

2015-09-03

Although the coupling of GC/MS with atmospheric pressure ionization (API) has been reported in 1970s, the interest in coupling GC with atmospheric pressure ion source was expanded in the last decade. The demand of a "soft" ion source for preserving highly diagnostic molecular ion is desirable, as compared to the "hard" ionization technique such as electron ionization (EI) in traditional GC/MS, which fragments the molecule in an extensive way. These API sources include atmospheric pressure chemical ionization (APCI), atmospheric pressure photoionization (APPI), atmospheric pressure laser ionization (APLI), electrospray ionization (ESI) and low temperature plasma (LTP). This review discusses the advantages and drawbacks of this analytical platform. After an introduction in atmospheric pressure ionization the review gives an overview about the history and explains the mechanisms of various atmospheric pressure ionization techniques used in combination with GC such as APCI, APPI, APLI, ESI and LTP. Also new developments made in ion source geometry, ion source miniaturization and multipurpose ion source constructions are discussed and a comparison between GC-FID, GC-EI-MS and GC-API-MS shows the advantages and drawbacks of these techniques. The review ends with an overview of applications realized with GC-API-MS. Copyright © 2015. Published by Elsevier B.V.

A Web-Based Interactive Mapping System of State Wide School Performance: Integrating Google Maps API Technology into Educational Achievement Data

ERIC Educational Resources Information Center

Wang, Kening; Mulvenon, Sean W.; Stegman, Charles; Anderson, Travis

2008-01-01

Google Maps API (Application Programming Interface), released in late June 2005 by Google, is an amazing technology that allows users to embed Google Maps in their own Web pages with JavaScript. Google Maps API has accelerated the development of new Google Maps based applications. This article reports a Web-based interactive mapping system…

Inhibiting DNA methylation alters olfactory extinction but not acquisition learning in Apis cerana and Apis mellifera.

PubMed

Gong, Zhiwen; Wang, Chao; Nieh, James C; Tan, Ken

2016-07-01

DNA methylation plays a key role in invertebrate acquisition and extinction memory. Honey bees have excellent olfactory learning, but the role of DNA methylation in memory formation has, to date, only been studied in Apis mellifera. We inhibited DNA methylation by inhibiting DNA methyltransferase (DNMT) with zebularine (zeb) and studied the resulting effects upon olfactory acquisition and extinction memory in two honey bee species, Apis cerana and A. mellifera. We used the proboscis extension reflex (PER) assay to measure memory. We provide the first demonstration that DNA methylation is also important in the olfactory extinction learning of A. cerana. DNMT did not reduce acquisition learning in either species. However, zeb bidirectionally and differentially altered extinction learning in both species. In particular, zeb provided 1h before acquisition learning improved extinction memory retention in A. mellifera, but reduced extinction memory retention in A. cerana. The reasons for these differences are unclear, but provide a basis for future studies to explore species-specific differences in the effects of methylation on memory formation. Copyright © 2016 Elsevier Ltd. All rights reserved.

A JEE RESTful service to access Conditions Data in ATLAS

NASA Astrophysics Data System (ADS)

Formica, Andrea; Gallas, E. J.

2015-12-01

Usage of condition data in ATLAS is extensive for offline reconstruction and analysis (e.g. alignment, calibration, data quality). The system is based on the LCG Conditions Database infrastructure, with read and write access via an ad hoc C++ API (COOL), a system which was developed before Run 1 data taking began. The infrastructure dictates that the data is organized into separate schemas (assigned to subsystems/groups storing distinct and independent sets of conditions), making it difficult to access information from several schemas at the same time. We have thus created PL/SQL functions containing queries to provide content extraction at multi-schema level. The PL/SQL API has been exposed to external clients by means of a Java application providing DB access via REST services, deployed inside an application server (JBoss WildFly). The services allow navigation over multiple schemas via simple URLs. The data can be retrieved either in XML or JSON formats, via simple clients (like curl or Web browsers).

Coordinating complex decision support activities across distributed applications

NASA Technical Reports Server (NTRS)

Adler, Richard M.

1994-01-01

Knowledge-based technologies have been applied successfully to automate planning and scheduling in many problem domains. Automation of decision support can be increased further by integrating task-specific applications with supporting database systems, and by coordinating interactions between such tools to facilitate collaborative activities. Unfortunately, the technical obstacles that must be overcome to achieve this vision of transparent, cooperative problem-solving are daunting. Intelligent decision support tools are typically developed for standalone use, rely on incompatible, task-specific representational models and application programming interfaces (API's), and run on heterogeneous computing platforms. Getting such applications to interact freely calls for platform independent capabilities for distributed communication, as well as tools for mapping information across disparate representations. Symbiotics is developing a layered set of software tools (called NetWorks! for integrating and coordinating heterogeneous distributed applications. he top layer of tools consists of an extensible set of generic, programmable coordination services. Developers access these services via high-level API's to implement the desired interactions between distributed applications.

Ionic liquids in drug delivery.

PubMed

Shamshina, Julia L; Barber, Patrick S; Rogers, Robin D

2013-10-01

To overcome potential problems with solid-state APIs, such as polymorphism, solubility and bioavailability, pure liquid salt (ionic liquid) forms of active pharmaceutical ingredients (API-ILs) are considered here as a design strategy. After a critical review of the current literature, the recent development of the API-ILs strategy is presented, with a particular focus on the liquefaction of drugs. A variety of IL tools for control over the liquid salt state of matter are discussed including choice of counterion to produce an IL from a given API; the concept of oligomeric ions that enables liquefaction of solid ILs by changing the stoichiometry or complexity of the ions; formation of 'liquid co-crystals' where hydrogen bonding is the driving force in the liquefaction of a neutral acid-base complex; combining an IL strategy with the prodrug strategy to improve the delivery of solid APIs; using ILs as delivery agents via trapping a drug in a micelle and finally ILs designed with tunable hydrophilic-lipophilic balance that matches the structural requirements needed to solubilize poorly water-soluble APIs. The authors believe that API-IL approaches may save failed lead candidates, extend the patent life of current APIs, lead to new delivery options or even new pharmaceutical action. They encourage the pharmaceutical industry to invest more research into the API-IL platform as it could lead to fast-tracked approval based on similarities to the APIs already approved.

Web Services--A Buzz Word with Potentials

Treesearch

János T. Füstös

2006-01-01

The simplest definition of a web service is an application that provides a web API. The web API exposes the functionality of the solution to other applications. The web API relies on other Internet-based technologies to manage communications. The resulting web services are pervasive, vendor-independent, language-neutral, and very low-cost. The main purpose of a web API...

Longevity extension of worker honey bees (Apis mellifera) by royal jelly: optimal dose and active ingredient

PubMed Central

Han, Mingfeng

2017-01-01

In the Western honey bee, Apis mellifera, queens and workers have different longevity although they share the same genome. Queens consume royal jelly (RJ) as the main food throughout their life, including as adults, but workers only eat worker jelly when they are larvae less than 3 days old. In order to explore the effect of RJ and the components affecting longevity of worker honey bees, we first determined the optimal dose for prolonging longevity of workers as 4% RJ in 50% sucrose solution, and developed a method of obtaining long lived workers. We then compared the effects of longevity extension by RJ 4% with bee-collected pollen from rapeseed (Brassica napus). Lastly, we determined that a water soluble RJ protein obtained by precipitation with 60% ammonium sulfate (RJP60) contained the main component for longevity extension after comparing the effects of RJ crude protein extract (RJCP), RJP30 (obtained by precipitation with 30% ammonium sulfate), and RJ ethanol extract (RJEE). Understanding what regulates worker longevity has potential to help increase colony productivity and improve crop pollination efficiency. PMID:28367370

Longevity extension of worker honey bees (Apis mellifera) by royal jelly: optimal dose and active ingredient.

PubMed

Yang, Wenchao; Tian, Yuanyuan; Han, Mingfeng; Miao, Xiaoqing

2017-01-01

In the Western honey bee, Apis mellifera , queens and workers have different longevity although they share the same genome. Queens consume royal jelly (RJ) as the main food throughout their life, including as adults, but workers only eat worker jelly when they are larvae less than 3 days old. In order to explore the effect of RJ and the components affecting longevity of worker honey bees, we first determined the optimal dose for prolonging longevity of workers as 4% RJ in 50% sucrose solution, and developed a method of obtaining long lived workers. We then compared the effects of longevity extension by RJ 4% with bee-collected pollen from rapeseed ( Brassica napus ). Lastly, we determined that a water soluble RJ protein obtained by precipitation with 60% ammonium sulfate (RJP 60 ) contained the main component for longevity extension after comparing the effects of RJ crude protein extract (RJCP), RJP 30 (obtained by precipitation with 30% ammonium sulfate), and RJ ethanol extract (RJEE). Understanding what regulates worker longevity has potential to help increase colony productivity and improve crop pollination efficiency.

Prioritizing pharmaceuticals in municipal wastewater

EPA Science Inventory

Oral presentation at SETAC North America 32nd annual meeting, describing our prioritization of active pharmaceutical ingredients (APIs), based on estimates of risks posed by API residues originating from municipal wastewater. Goals of this project include prioritization of APIs f...

Measuring the impact of an API-first mentality with ScienceBase after 4.5 years

NASA Astrophysics Data System (ADS)

Bristol, S.; Tekell, S.

2016-12-01

ScienceBase is a research infrastructure developed and operated by the U.S. Geological Survey with users and uses across a number of other agency and organization partners. Over four years ago, we released an Application Programming Interface (API) as the foundation of the system and took on the mindset that our progress would be measured by the uptake of the API by others beyond ourselves in developing interesting applications. We now measure success more by someone finding ScienceBase, organizing their data and information, developing an innovative API-driven application and then serendipitous discovery through a science meeting. Because of the way we built the RESTful API, we can characterize what parts of the system are employed. Analysis of usage data helps us take the supposition out of what works and guides design and funding decisions. This analytics-based process facilitates regular adjustments to our thinking and allows us to test design decisions as hypotheses rather than untestable aspirations.

Development of NETCONF-Based Network Management Systems in Web Services Framework

NASA Astrophysics Data System (ADS)

Iijima, Tomoyuki; Kimura, Hiroyasu; Kitani, Makoto; Atarashi, Yoshifumi

To develop a network management system (NMS) more easily, the authors developed an application programming interface (API) for configuring network devices. Because this API is used in a Java development environment, an NMS can be developed by utilizing the API and other commonly available Java libraries. It is thus possible to easily develop an NMS that is highly compatible with other IT systems. And operations that are generated from the API and that are exchanged between the NMS and network devices are based on NETCONF, which is standardized by the Internet Engineering Task Force (IETF) as a next-generation network-configuration protocol. Adopting a standardized technology ensures that the NMS developed by using the API can manage network devices provided from multi-vendors in a unified manner. Furthermore, the configuration items exchanged over NETCONF are specified in an object-oriented design. They are therefore easier to manage than such items in the Management Information Base (MIB), which is defined as data to be managed by the Simple Network Management Protocol (SNMP). We actually developed several NMSs by using the API. Evaluation of these NMSs showed that, in terms of configuration time and development time, the NMS developed by using the API performed as well as NMSs developed by using a command line interface (CLI) and SNMP. The NMS developed by using the API showed feasibility to achieve “autonomic network management” and “high interoperability with IT systems.”

Honeybees (Apis mellifera) learn to discriminate the smell of organic compounds from their respective deuterated isotopomers

PubMed Central

Gronenberg, Wulfila; Raikhelkar, Ajay; Abshire, Eric; Stevens, Jennifer; Epstein, Eric; Loyola, Karin; Rauscher, Michael; Buchmann, Stephen

2014-01-01

The understanding of physiological and molecular processes underlying the sense of smell has made considerable progress during the past three decades, revealing the cascade of molecular steps that lead to the activation of olfactory receptor (OR) neurons. However, the mode of primary interaction of odorant molecules with the OR proteins within the sensory cells is still enigmatic. Two different concepts try to explain these interactions: the ‘odotope hypothesis’ suggests that OR proteins recognize structural aspects of the odorant molecule, whereas the ‘vibration hypothesis’ proposes that intra-molecular vibrations are the basis for the recognition of the odorant by the receptor protein. The vibration hypothesis predicts that OR proteins should be able to discriminate compounds containing deuterium from their common counterparts which contain hydrogen instead of deuterium. This study tests this prediction in honeybees (Apis mellifera) using the proboscis extension reflex learning in a differential conditioning paradigm. Rewarding one odour (e.g. a deuterated compound) with sucrose and not rewarding the respective analogue (e.g. hydrogen-based odorant) shows that honeybees readily learn to discriminate hydrogen-based odorants from their deuterated counterparts and supports the idea that intra-molecular vibrations may contribute to odour discrimination. PMID:24452031

Multi-National Information Sharing -- Cross Domain Collaborative Information Environment (CDCIE) Solution. Revision 4

DTIC Science & Technology

2005-04-12

Hardware, Database, and Operating System independence using Java • Enterprise-class Architecture using Java2 Enterprise Edition 1.4 • Standards based...portal applications. Compliance with the Java Specification Request for Portlet APIs (JSR-168) (Portlet API) and Web Services for Remote Portals...authentication and authorization • Portal Standards using Java Specification Request for Portlet APIs (JSR-168) (Portlet API) and Web Services for Remote

Doclet To Synthesize UML

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

The RoseDoclet computer program extends the capability of Java doclet software to automatically synthesize Unified Modeling Language (UML) content from Java language source code. [Doclets are Java-language programs that use the doclet application programming interface (API) to specify the content and format of the output of Javadoc. Javadoc is a program, originally designed to generate API documentation from Java source code, now also useful as an extensible engine for processing Java source code.] RoseDoclet takes advantage of Javadoc comments and tags already in the source code to produce a UML model of that code. RoseDoclet applies the doclet API to create a doclet passed to Javadoc. The Javadoc engine applies the doclet to the source code, emitting the output format specified by the doclet. RoseDoclet emits a Rose model file and populates it with fully documented packages, classes, methods, variables, and class diagrams identified in the source code. The way in which UML models are generated can be controlled by use of new Javadoc comment tags that RoseDoclet provides. The advantage of using RoseDoclet is that Javadoc documentation becomes leveraged for two purposes: documenting the as-built API and keeping the design documentation up to date.

Integrative Advanced Oxidation and Biofiltration for Treating Pharmaceuticals in Wastewater.

PubMed

Lester, Yaal; Aga, Diana S; Love, Nancy G; Singh, Randolph R; Morrissey, Ian; Linden, Karl G

2016-11-01

  Advanced oxidation of active pharmaceutical ingredients (APIs) in wastewater produces transformation products (TPs) that are often more biodegradable than the parent compounds. Secondary effluent from a wastewater treatment plant was treated using UV-based advanced oxidation (LPUV/H2O2 and MPUV/NO3) followed by biological aerated filtration (BAF), and different APIs and their transformation products were monitored. The advanced oxidation processes degraded the APIs by 55-87% (LPUV/H2O2) and 58-95% (MPUV/NO3), while minor loss of APIs was achieved in the downstream BAF system. Eleven TPs were detected following oxidation of carbamazepine (5) and iopromide (6); three key TPs were biodegraded in the BAF system. The other TPs remained relatively constant in the BAF. The decrease in UV absorbance (UVA254) of the effluent in the BAF system was linearly correlated to the degradation of the APIs (for the MPUV/NO3-BAF), and can be applied to monitor the biotransformation of APIs in biological-based systems.

A Development of Lightweight Grid Interface

NASA Astrophysics Data System (ADS)

Iwai, G.; Kawai, Y.; Sasaki, T.; Watase, Y.

2011-12-01

In order to help a rapid development of Grid/Cloud aware applications, we have developed API to abstract the distributed computing infrastructures based on SAGA (A Simple API for Grid Applications). SAGA, which is standardized in the OGF (Open Grid Forum), defines API specifications to access distributed computing infrastructures, such as Grid, Cloud and local computing resources. The Universal Grid API (UGAPI), which is a set of command line interfaces (CLI) and APIs, aims to offer simpler API to combine several SAGA interfaces with richer functionalities. These CLIs of the UGAPI offer typical functionalities required by end users for job management and file access to the different distributed computing infrastructures as well as local computing resources. We have also built a web interface for the particle therapy simulation and demonstrated the large scale calculation using the different infrastructures at the same time. In this paper, we would like to present how the web interface based on UGAPI and SAGA achieve more efficient utilization of computing resources over the different infrastructures with technical details and practical experiences.

Pharmaceuticals in water, fish and osprey nestlings in Delaware River and Bay

USGS Publications Warehouse

Bean, Thomas G.; Rattner, Barnett A.; Lazarus, Rebecca S.; Day, Daniel D.; Burket, S. Rebekah; Brooks, Bryan W.; Haddad, Samuel P.; Bowerman, William W.

2018-01-01

Exposure of wildlife to Active Pharmaceutical Ingredients (APIs) is likely to occur but studies of risk are limited. One exposure pathway that has received attention is trophic transfer of APIs in a water-fish-osprey food chain. Samples of water, fish plasma and osprey plasma were collected from Delaware River and Bay, and analyzed for 21 APIs. Only 2 of 21 analytes exceeded method detection limits in osprey plasma (acetaminophen and diclofenac) with plasma levels typically 2–3 orders of magnitude below human therapeutic concentrations (HTC). We built upon a screening level model used to predict osprey exposure to APIs in Chesapeake Bay and evaluated whether exposure levels could have been predicted in Delaware Bay had we just measured concentrations in water or fish. Use of surface water and BCFs did not predict API concentrations in fish well, likely due to fish movement patterns, and partitioning and bioaccumulation uncertainties associated with these ionizable chemicals. Input of highest measured API concentration in fish plasma combined with pharmacokinetic data accurately predicted that diclofenac and acetaminophen would be the APIs most likely detected in osprey plasma. For the majority of APIs modeled, levels were not predicted to exceed 1 ng/mL or method detection limits in osprey plasma. Based on the target analytes examined, there is little evidence that APIs represent a significant risk to ospreys nesting in Delaware Bay. If an API is present in fish orders of magnitude below HTC, sampling of fish-eating birds is unlikely to be necessary. However, several human pharmaceuticals accumulated in fish plasma within a recommended safety factor for HTC. It is now important to expand the scope of diet-based API exposure modeling to include alternative exposure pathways (e.g., uptake from landfills, dumps and wastewater treatment plants) and geographic locations (developing countries) where API contamination of the environment may represent greater risk.

In-line UV spectroscopy for the quantification of low-dose active ingredients during the manufacturing of pharmaceutical semi-solid and liquid formulations.

PubMed

Bostijn, N; Hellings, M; Van Der Veen, M; Vervaet, C; De Beer, T

2018-07-12

UltraViolet (UV) spectroscopy was evaluated as an innovative Process Analytical Technology (PAT) - tool for the in-line and real-time quantitative determination of low-dosed active pharmaceutical ingredients (APIs) in a semi-solid (gel) and a liquid (suspension) pharmaceutical formulation during their batch production process. The performance of this new PAT-tool (i.e., UV spectroscopy) was compared with an already more established PAT-method based on Raman spectroscopy. In-line UV measurements were carried out with an immersion probe while for the Raman measurements a non-contact PhAT probe was used. For both studied formulations, an in-line API quantification model was developed and validated per spectroscopic technique. The known API concentrations (Y) were correlated with the corresponding in-line collected preprocessed spectra (X) through a Partial Least Squares (PLS) regression. Each developed quantification method was validated by calculating the accuracy profile on the basis of the validation experiments. Furthermore, the measurement uncertainty was determined based on the data generated for the determination of the accuracy profiles. From the accuracy profile of the UV- and Raman-based quantification method for the gel, it was concluded that at the target API concentration of 2% (w/w), 95 out of 100 future routine measurements given by the Raman method will not deviate more than 10% (relative error) from the true API concentration, whereas for the UV method the acceptance limits of 10% were exceeded. For the liquid formulation, the Raman method was not able to quantify the API in the low-dosed suspension (0.09% (w/w) API). In contrast, the in-line UV method was able to adequately quantify the API in the suspension. This study demonstrated that UV spectroscopy can be adopted as a novel in-line PAT-technique for low-dose quantification purposes in pharmaceutical processes. Important is that none of the two spectroscopic techniques was superior to the other for both formulations: the Raman method was more accurate in quantifying the API in the gel (2% (w/w) API), while the UV method performed better for API quantification in the suspension (0.09% (w/w) API). Copyright © 2018 Elsevier B.V. All rights reserved.

NSLS-II HIGH LEVEL APPLICATION INFRASTRUCTURE AND CLIENT API DESIGN

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

Shen, G.; Yang; L.

2011-03-28

The beam commissioning software framework of NSLS-II project adopts a client/server based architecture to replace the more traditional monolithic high level application approach. It is an open structure platform, and we try to provide a narrow API set for client application. With this narrow API, existing applications developed in different language under different architecture could be ported to our platform with small modification. This paper describes system infrastructure design, client API and system integration, and latest progress. As a new 3rd generation synchrotron light source with ultra low emittance, there are new requirements and challenges to control and manipulate themore » beam. A use case study and a theoretical analysis have been performed to clarify requirements and challenges to the high level applications (HLA) software environment. To satisfy those requirements and challenges, adequate system architecture of the software framework is critical for beam commissioning, study and operation. The existing traditional approaches are self-consistent, and monolithic. Some of them have adopted a concept of middle layer to separate low level hardware processing from numerical algorithm computing, physics modelling, data manipulating, plotting, and error handling. However, none of the existing approaches can satisfy the requirement. A new design has been proposed by introducing service oriented architecture technology. The HLA is combination of tools for accelerator physicists and operators, which is same as traditional approach. In NSLS-II, they include monitoring applications and control routines. Scripting environment is very important for the later part of HLA and both parts are designed based on a common set of APIs. Physicists and operators are users of these APIs, while control system engineers and a few accelerator physicists are the developers of these APIs. With our Client/Server mode based approach, we leave how to retrieve information to the developers of APIs and how to use them to form a physics application to the users. For example, how the channels are related to magnet and what the current real-time setting of a magnet is in physics unit are the internals of APIs. Measuring chromaticities are the users of APIs. All the users of APIs are working with magnet and instrument names in a physics unit. The low level communications in current or voltage unit are minimized. In this paper, we discussed our recent progress of our infrastructure development, and client API.« less

The proboscis extension reflex to evaluate learning and memory in honeybees ( Apis mellifera): some caveats

NASA Astrophysics Data System (ADS)

Frost, Elisabeth H.; Shutler, Dave; Hillier, Neil Kirk

2012-09-01

The proboscis extension reflex (PER) is widely used in a classical conditioning (Pavlovian) context to evaluate learning and memory of a variety of insect species. The literature is particularly prodigious for honeybees ( Apis mellifera) with more than a thousand publications. Imagination appears to be the only limit to the types of challenges to which researchers subject honeybees, including all the sensory modalities and a broad diversity of environmental treatments. Accordingly, some remarkable insights have been achieved using PER. However, there are several challenges to evaluating the PER literature that warrant a careful and thorough review. We assess here variation in methods that makes interpretation of studies, even those researching the same question, tenuous. We suggest that the numerous variables that might influence experimental outcomes from PER be thoroughly detailed by researchers. Moreover, the influence of individual variables on results needs to carefully evaluated, as well as among two or more variables. Our intent is to encourage investigation of the influence of numerous variables on PER results.

Spatial and temporal analysis of Air Pollution Index and its timescale-dependent relationship with meteorological factors in Guangzhou, China, 2001-2011.

PubMed

Li, Li; Qian, Jun; Ou, Chun-Quan; Zhou, Ying-Xue; Guo, Cui; Guo, Yuming

2014-07-01

There is an increasing interest in spatial and temporal variation of air pollution and its association with weather conditions. We presented the spatial and temporal variation of Air Pollution Index (API) and examined the associations between API and meteorological factors during 2001-2011 in Guangzhou, China. A Seasonal-Trend Decomposition Procedure Based on Loess (STL) was used to decompose API. Wavelet analyses were performed to examine the relationships between API and several meteorological factors. Air quality has improved since 2005. APIs were highly correlated among five monitoring stations, and there were substantial temporal variations. Timescale-dependent relationships were found between API and a variety of meteorological factors. Temperature, relative humidity, precipitation and wind speed were negatively correlated with API, while diurnal temperature range and atmospheric pressure were positively correlated with API in the annual cycle. Our findings should be taken into account when determining air quality forecasts and pollution control measures. Copyright © 2014 Elsevier Ltd. All rights reserved.

A JavaScript API for the Ice Sheet System Model (ISSM) 4.11: towards an online interactive model for the cryosphere community

NASA Astrophysics Data System (ADS)

Larour, Eric; Cheng, Daniel; Perez, Gilberto; Quinn, Justin; Morlighem, Mathieu; Duong, Bao; Nguyen, Lan; Petrie, Kit; Harounian, Silva; Halkides, Daria; Hayes, Wayne

2017-12-01

Earth system models (ESMs) are becoming increasingly complex, requiring extensive knowledge and experience to deploy and use in an efficient manner. They run on high-performance architectures that are significantly different from the everyday environments that scientists use to pre- and post-process results (i.e., MATLAB, Python). This results in models that are hard to use for non-specialists and are increasingly specific in their application. It also makes them relatively inaccessible to the wider science community, not to mention to the general public. Here, we present a new software/model paradigm that attempts to bridge the gap between the science community and the complexity of ESMs by developing a new JavaScript application program interface (API) for the Ice Sheet System Model (ISSM). The aforementioned API allows cryosphere scientists to run ISSM on the client side of a web page within the JavaScript environment. When combined with a web server running ISSM (using a Python API), it enables the serving of ISSM computations in an easy and straightforward way. The deep integration and similarities between all the APIs in ISSM (MATLAB, Python, and now JavaScript) significantly shortens and simplifies the turnaround of state-of-the-art science runs and their use by the larger community. We demonstrate our approach via a new Virtual Earth System Laboratory (VESL) website (http://vesl.jpl.nasa.gov, VESL(2017)).

Classical conditioning of proboscis extension in harnessed Africanized honey bee queens (Apis mellifera L.).

PubMed

Aquino, Italo S; Abramson, Charles I; Soares, Ademilson E E; Fernandes, Andrea Cardoso; Benbassat, Danny

2004-06-01

Experiments are reported on learning in virgin Africanized honey bee queens (Apis mellifera L.). Queens restrained in a "Pavlovian harness" received a pairing of hexanal odor with a 1.8-M feeding of sucrose solution. Compared to explicitly unpaired controls, acquisition was rapid in reaching about 90%. Acquisition was also rapid in queens receiving an unconditioned stimulus of "bee candy" or an unconditioned stimulus administered by worker bees. During extinction the conditioned response declines. The steepest decline was observed in queens receiving an unconditioned stimulus of bee candy. These findings extend previous work on learning of Afrianized honey bee workers to a population of queen bees.

uPy: a ubiquitous computer graphics Python API with Biological Modeling Applications

PubMed Central

Autin, L.; Johnson, G.; Hake, J.; Olson, A.; Sanner, M.

2015-01-01

In this paper we describe uPy, an extension module for the Python programming language that provides a uniform abstraction of the APIs of several 3D computer graphics programs called hosts, including: Blender, Maya, Cinema4D, and DejaVu. A plugin written with uPy is a unique piece of code that will run in all uPy-supported hosts. We demonstrate the creation of complex plug-ins for molecular/cellular modeling and visualization and discuss how uPy can more generally simplify programming for many types of projects (not solely science applications) intended for multi-host distribution. uPy is available at http://upy.scripps.edu PMID:24806987

Effects of Bacillus thuringiensis strains virulent to Varroa destructor on larvae and adults of Apis mellifera.

PubMed

Alquisira-Ramírez, Eva Vianey; Peña-Chora, Guadalupe; Hernández-Velázquez, Víctor Manuel; Alvear-García, Andrés; Arenas-Sosa, Iván; Suarez-Rodríguez, Ramón

2017-08-01

The sublethal effects of two strains of Bacillus thuringiensis, which were virulent in vitro to Varroa destructor, were measured on Apis mellifera. The effects of five concentrations of total protein (1, 5, 25, 50 and 100μg/mL) from the EA3 and EA26.1 strains on larval and adult honey bees were evaluated for two and seven days under laboratory conditions. Based on the concentrations evaluated, total protein from the two strains did not affect the development of larvae, the syrup consumption, locomotor activity or proboscis extension response of adults. These same parameters were also tested for the effects of three concentrations (1, 10 and 15μg/kg) of cypermethrin as a positive control. Although no significant differences were observed after two days of treatment with cypermethrin, a dose-response relationship in syrup consumption and locomotor activity was observed. A significant reduction in the proboscis extension response of the bees treated with cypermethrin was also observed. Therefore, in contrast to cypermethrin, our results indicate that the EA3 and EA26.1 strains of B. thuringiensis can be used in beehives to control V. destructor and reduce the negative effects of this mite on colonies without adverse effects on the larvae and adults of A. mellifera. Additionally, the overuse of synthetic miticides, which produce both lethal and sublethal effects on bees, can be reduced. Copyright © 2017 Elsevier Inc. All rights reserved.

Forward and Backward Second-Order Pavlovian Conditioning in Honeybees

ERIC Educational Resources Information Center

Hussaini, Syed Abid; Komischke, Bernhard; Menzel, Randolf; Lachnit, Harald

2007-01-01

Second-order conditioning (SOC) is the association of a neutral stimulus with another stimulus that had previously been combined with an unconditioned stimulus (US). We used classical conditioning of the proboscis extension response (PER) in honeybees ("Apis mellifera") with odors (CS) and sugar (US). Previous SOC experiments in bees were…

Programmatic access to logical models in the Cell Collective modeling environment via a REST API.

PubMed

Kowal, Bryan M; Schreier, Travis R; Dauer, Joseph T; Helikar, Tomáš

2016-01-01

Cell Collective (www.cellcollective.org) is a web-based interactive environment for constructing, simulating and analyzing logical models of biological systems. Herein, we present a Web service to access models, annotations, and simulation data in the Cell Collective platform through the Representational State Transfer (REST) Application Programming Interface (API). The REST API provides a convenient method for obtaining Cell Collective data through almost any programming language. To ensure easy processing of the retrieved data, the request output from the API is available in a standard JSON format. The Cell Collective REST API is freely available at http://thecellcollective.org/tccapi. All public models in Cell Collective are available through the REST API. For users interested in creating and accessing their own models through the REST API first need to create an account in Cell Collective (http://thecellcollective.org). thelikar2@unl.edu. Technical user documentation: https://goo.gl/U52GWo. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

JEnsembl: a version-aware Java API to Ensembl data systems.

PubMed

Paterson, Trevor; Law, Andy

2012-11-01

The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing 'through time' comparative analyses to be performed. Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net).

Context-Based Mobile Security Enclave

DTIC Science & Technology

2012-09-01

29  c.  Change IMSI .............................30  d.  Change CellID ...........................31  e.  Change Geolocation ...Assisted Global Positioning System ADB Android Debugger API Application Programming Interface APK Android Application Package BSC Base Station...Programming Interfaces ( APIs ), which use Java compatible libraries based on Apache Harmony (an open source Java implementation developed by the Apache

Physicochemical characterisation and investigation of the bonding mechanisms of API-titanate nanotube composites as new drug carrier systems.

PubMed

Sipos, Barbara; Pintye-Hódi, Klára; Kónya, Zoltán; Kelemen, András; Regdon, Géza; Sovány, Tamás

2017-02-25

Titanate nanotube (TNT) has recently been explored as a new carrier material for active pharmaceutical ingredients (API). The aim of the present work was to reveal the physicochemical properties of API-TNT composites, focusing on the interactions between the TNTs and the incorporated APIs. Drugs belonging to different Biopharmaceutical Classification System (BCS) classes were loaded into TNTs: diltiazem hydrochloride (BCS I.), diclofenac sodium (BCS II.), atenolol (BCS III.) and hydrochlorothiazide (BCS IV.). Experimental results demonstrated that it is feasible for spiral cross-sectioned titanate nanotubes to carry drugs and maintain their bioactivity. The structural properties of the composites were characterized by a range of analytical techniques, including FT-IR, DSC, TG-MS, etc. The interactions between APIs and TNTs were identified as electrostatic attractions, mainly dominated by hydrogen bonds. Based on the results, it can be stated that the strength of the association depends on the hydrogen donor strength of the API. The drug release of incorporated APIs was evaluated from compressed tablets and compared to that of pure APIs. Differences noticed in the dissolution profiles due to incorporation showed a correlation with the strength of interactions between the APIs and the TNTs observed in the above analytical studies. Copyright © 2016 Elsevier B.V. All rights reserved.

Similar English Learner Students, Different Results: Why Do Some Schools Do Better? A Follow-Up Analysis Based upon a Large-Scale Survey of California Elementary Schools Serving High Proportions of Low-Income and EL Students. Report of Findings

ERIC Educational Resources Information Center

Williams, Trish; Perry, Mary; Oregon, Isabel; Brazil, Noli; Hakuta, Kenji; Haertel, Edward; Kirst, Michael; Levin, Jesse

2007-01-01

In Spring 2006 California released its first ever school-level Academic Performance Index (API) scores for English Learners (ELs). These EL-API scores were based on California Standards Tests in English language arts and math taken in the spring of 2005. The new EL-API data make it clear that elementary schools vary widely in their ability to get…

Runtime Performance Monitoring Tool for RTEMS System Software

NASA Astrophysics Data System (ADS)

Cho, B.; Kim, S.; Park, H.; Kim, H.; Choi, J.; Chae, D.; Lee, J.

2007-08-01

RTEMS is a commercial-grade real-time operating system that supports multi-processor computers. However, there are not many development tools for RTEMS. In this paper, we report new RTEMS-based runtime performance monitoring tool. We have implemented a light weight runtime monitoring task with an extension to the RTEMS APIs. Using our tool, software developers can verify various performance- related parameters during runtime. Our tool can be used during software development phase and in-orbit operation as well. Our implemented target agent is light weight and has small overhead using SpaceWire interface. Efforts to reduce overhead and to add other monitoring parameters are currently under research.

A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton.

PubMed

Nunez-Iglesias, Juan; Blanch, Adam J; Looker, Oliver; Dixon, Matthew W; Tilley, Leann

2018-01-01

We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the "analyse skeletons" plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan's measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions.

A new Python library to analyse skeleton images confirms malaria parasite remodelling of the red blood cell membrane skeleton

PubMed Central

Looker, Oliver; Dixon, Matthew W.; Tilley, Leann

2018-01-01

We present Skan (Skeleton analysis), a Python library for the analysis of the skeleton structures of objects. It was inspired by the “analyse skeletons” plugin for the Fiji image analysis software, but its extensive Application Programming Interface (API) allows users to examine and manipulate any intermediate data structures produced during the analysis. Further, its use of common Python data structures such as SciPy sparse matrices and pandas data frames opens the results to analysis within the extensive ecosystem of scientific libraries available in Python. We demonstrate the validity of Skan’s measurements by comparing its output to the established Analyze Skeletons Fiji plugin, and, with a new scanning electron microscopy (SEM)-based method, we confirm that the malaria parasite Plasmodium falciparum remodels the host red blood cell cytoskeleton, increasing the average distance between spectrin-actin junctions. PMID:29472997

Mechanism of action of recombinant Acc-royalisin from royal jelly of Chinese honeybee against gram-positive bacteria

USDA-ARS?s Scientific Manuscript database

The antibacterial activity of royalisin, an antimicrobial peptide from the royal jelly produced by honeybees has been addressed extensively. However, its mechanism of action remains unclear. In this study, a recombinant royalisin, RAcc-royalisin from the royal jelly of Chinese honeybee Apis cerana...

Antimicrobial activity of honey of africanized bee (Apis mellifera) and stingless bee, tiuba (Melipona fasciculata) against strains of Escherichia coli, Pseudomona aeruginosa and Staphylococcus aureus

NASA Astrophysics Data System (ADS)

Tenório, Eleuza Gomes; Alves, Natália Furtado; Mendes, Bianca Evanita Pimenta

2017-11-01

The objective of this study was to investigate the antimicrobial activity of honey of Africanized bees (Apis mellifera) and stingless bees (Melipona fasciculata), produced under the same flowering conditions, in municipalities of Baixada Maranhese, Brazil, against strains of pathogenic bacteria, Escherichia coli, Pseudomonas aeruginosa and Staphylococcus aureus. In each municipality, the apiary and meliponario were less than 150 meters away from each other. The Kirby-Bauer method, and the diffusion technique of the agar plate through the extension of the inhibition in millimeters were used. The test results were negative for all samples, which did not demonstrate antimicrobial activity in any of the microorganisms tested.

The Ruby UCSC API: accessing the UCSC genome database using Ruby.

PubMed

Mishima, Hiroyuki; Aerts, Jan; Katayama, Toshiaki; Bonnal, Raoul J P; Yoshiura, Koh-ichiro

2012-09-21

The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast.The API uses the bin index-if available-when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/.

The Ruby UCSC API: accessing the UCSC genome database using Ruby

PubMed Central

2012-01-01

Background The University of California, Santa Cruz (UCSC) genome database is among the most used sources of genomic annotation in human and other organisms. The database offers an excellent web-based graphical user interface (the UCSC genome browser) and several means for programmatic queries. A simple application programming interface (API) in a scripting language aimed at the biologist was however not yet available. Here, we present the Ruby UCSC API, a library to access the UCSC genome database using Ruby. Results The API is designed as a BioRuby plug-in and built on the ActiveRecord 3 framework for the object-relational mapping, making writing SQL statements unnecessary. The current version of the API supports databases of all organisms in the UCSC genome database including human, mammals, vertebrates, deuterostomes, insects, nematodes, and yeast. The API uses the bin index—if available—when querying for genomic intervals. The API also supports genomic sequence queries using locally downloaded *.2bit files that are not stored in the official MySQL database. The API is implemented in pure Ruby and is therefore available in different environments and with different Ruby interpreters (including JRuby). Conclusions Assisted by the straightforward object-oriented design of Ruby and ActiveRecord, the Ruby UCSC API will facilitate biologists to query the UCSC genome database programmatically. The API is available through the RubyGem system. Source code and documentation are available at https://github.com/misshie/bioruby-ucsc-api/ under the Ruby license. Feedback and help is provided via the website at http://rubyucscapi.userecho.com/. PMID:22994508

Adaptive Approximation-Based Regulation Control for a Class of Uncertain Nonlinear Systems Without Feedback Linearizability.

PubMed

Wang, Ning; Sun, Jing-Chao; Han, Min; Zheng, Zhongjiu; Er, Meng Joo

2017-09-06

In this paper, for a general class of uncertain nonlinear (cascade) systems, including unknown dynamics, which are not feedback linearizable and cannot be solved by existing approaches, an innovative adaptive approximation-based regulation control (AARC) scheme is developed. Within the framework of adding a power integrator (API), by deriving adaptive laws for output weights and prediction error compensation pertaining to single-hidden-layer feedforward network (SLFN) from the Lyapunov synthesis, a series of SLFN-based approximators are explicitly constructed to exactly dominate completely unknown dynamics. By the virtue of significant advancements on the API technique, an adaptive API methodology is eventually established in combination with SLFN-based adaptive approximators, and it contributes to a recursive mechanism for the AARC scheme. As a consequence, the output regulation error can asymptotically converge to the origin, and all other signals of the closed-loop system are uniformly ultimately bounded. Simulation studies and comprehensive comparisons with backstepping- and API-based approaches demonstrate that the proposed AARC scheme achieves remarkable performance and superiority in dealing with unknown dynamics.

Development and validation of an in-line NIR spectroscopic method for continuous blend potency determination in the feed frame of a tablet press.

PubMed

De Leersnyder, Fien; Peeters, Elisabeth; Djalabi, Hasna; Vanhoorne, Valérie; Van Snick, Bernd; Hong, Ke; Hammond, Stephen; Liu, Angela Yang; Ziemons, Eric; Vervaet, Chris; De Beer, Thomas

2018-03-20

A calibration model for in-line API quantification based on near infrared (NIR) spectra collection during tableting in the tablet press feed frame was developed and validated. First, the measurement set-up was optimised and the effect of filling degree of the feed frame on the NIR spectra was investigated. Secondly, a predictive API quantification model was developed and validated by calculating the accuracy profile based on the analysis results of validation experiments. Furthermore, based on the data of the accuracy profile, the measurement uncertainty was determined. Finally, the robustness of the API quantification model was evaluated. An NIR probe (SentroPAT FO) was implemented into the feed frame of a rotary tablet press (Modul™ P) to monitor physical mixtures of a model API (sodium saccharine) and excipients with two different API target concentrations: 5 and 20% (w/w). Cutting notches into the paddle wheel fingers did avoid disturbances of the NIR signal caused by the rotating paddle wheel fingers and hence allowed better and more complete feed frame monitoring. The effect of the design of the notched paddle wheel fingers was also investigated and elucidated that straight paddle wheel fingers did cause less variation in NIR signal compared to curved paddle wheel fingers. The filling degree of the feed frame was reflected in the raw NIR spectra. Several different calibration models for the prediction of the API content were developed, based on the use of single spectra or averaged spectra, and using partial least squares (PLS) regression or ratio models. These predictive models were then evaluated and validated by processing physical mixtures with different API concentrations not used in the calibration models (validation set). The β-expectation tolerance intervals were calculated for each model and for each of the validated API concentration levels (β was set at 95%). PLS models showed the best predictive performance. For each examined saccharine concentration range (i.e., between 4.5 and 6.5% and between 15 and 25%), at least 95% of future measurements will not deviate more than 15% from the true value. Copyright © 2018 Elsevier B.V. All rights reserved.

Recombinant allergen-based IgE testing to distinguish bee and wasp allergy.

PubMed

Mittermann, Irene; Zidarn, Mihaela; Silar, Mira; Markovic-Housley, Zora; Aberer, Werner; Korosec, Peter; Kosnik, Mitja; Valenta, Rudolf

2010-06-01

The identification of the disease-causing insect in venom allergy is often difficult. To establish recombinant allergen-based IgE tests to diagnose bee and yellow jacket wasp allergy. Sera from patients with bee and/or wasp allergy (n = 43) and patients with pollen allergy with false-positive IgE serology to venom extracts were tested for IgE reactivity in allergen extract-based tests or with purified allergens, including nonglycosylated Escherichia coli-expressed recombinant (r) Api m 1, rApi m 2, rVes v 5, and insect cell-expressed, glycosylated rApi m 2 as well as 2 natural plant glycoproteins (Phl p 4, bromelain). The patients with venom allergy could be diagnosed with a combination of E coli-expressed rApi m 1, rApi m 2, and rVes v 5 whereas patients with pollen allergy remained negative. For a group of 29 patients for whom the sensitizing venom could not be identified with natural allergen extracts, testing with nonglycosylated allergens allowed identification of the sensitizing venom. Recombinant nonglycosylated allergens also allowed definition of the sensitizing venom for those 14 patients who had reacted either with bee or wasp venom extracts. By IgE inhibition studies, it is shown that glycosylated Api m 2 contains carbohydrate epitopes that cross-react with natural Api m 1, Ves v 2, natural Phl p 4, and bromelain, thus identifying cross-reactive structures responsible for serologic false-positive test results or double-positivity to bee and wasp extracts. Nonglycosylated recombinant bee and wasp venom allergens allow the identification of patients with bee and wasp allergy and should facilitate accurate prescription of venom immunotherapy. Copyright (c) 2010 American Academy of Allergy, Asthma & Immunology. Published by Mosby, Inc. All rights reserved.

Developing Cancer Informatics Applications and Tools Using the NCI Genomic Data Commons API.

PubMed

Wilson, Shane; Fitzsimons, Michael; Ferguson, Martin; Heath, Allison; Jensen, Mark; Miller, Josh; Murphy, Mark W; Porter, James; Sahni, Himanso; Staudt, Louis; Tang, Yajing; Wang, Zhining; Yu, Christine; Zhang, Junjun; Ferretti, Vincent; Grossman, Robert L

2017-11-01

The NCI Genomic Data Commons (GDC) was launched in 2016 and makes available over 4 petabytes (PB) of cancer genomic and associated clinical data to the research community. This dataset continues to grow and currently includes over 14,500 patients. The GDC is an example of a biomedical data commons, which collocates biomedical data with storage and computing infrastructure and commonly used web services, software applications, and tools to create a secure, interoperable, and extensible resource for researchers. The GDC is (i) a data repository for downloading data that have been submitted to it, and also a system that (ii) applies a common set of bioinformatics pipelines to submitted data; (iii) reanalyzes existing data when new pipelines are developed; and (iv) allows users to build their own applications and systems that interoperate with the GDC using the GDC Application Programming Interface (API). We describe the GDC API and how it has been used both by the GDC itself and by third parties. Cancer Res; 77(21); e15-18. ©2017 AACR . ©2017 American Association for Cancer Research.

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

Welcome, Michael L.; Bell, Christian S.

GASNet (Global-Address Space Networking) is a language-independent, low-level networking layer that provides network-independent, high-performance communication primitives tailored for implementing parallel global address space SPMD languages such as UPC and Titanium. The interface is primarily intended as a compilation target and for use by runtime library writers (as opposed to end users), and the primary goals are high performance, interface portability, and expressiveness. GASNet is designed specifically to support high-performance, portable implementations of global address space languages on modern high-end communication networks. The interface provides the flexibility and extensibility required to express a wide variety of communication patterns without sacrificing performancemore » by imposing large computational overheads in the interface. The design of the GASNet interface is partitioned into two layers to maximize porting ease without sacrificing performance: the lower level is a narrow but very general interface called the GASNet core API - the design is basedheavily on Active Messages, and is implemented directly on top of each individual network architecture. The upper level is a wider and more expressive interface called GASNet extended API, which provides high-level operations such as remote memory access and various collective operations. This release implements GASNet over MPI, the Quadrics "elan" API, the Myrinet "GM" API and the "LAPI" interface to the IBM SP switch. A template is provided for adding support for additional network interfaces.« less

A study of the feasibility and performance of an active/passive imager using silicon focal plane arrays and incoherent continuous wave laser diodes

NASA Astrophysics Data System (ADS)

Vollmerhausen, Richard H.

This dissertation describes an active/passive imager (API) that provides reliable, nighttime, target acquisition in a man-portable package with effective visual range of about 4 kilometers. The reflective imagery is easier to interpret than currently used thermal imagery. Also, in the active mode, the API provides performance equivalent to the big-aperture, thermal systems used on weapons platforms like tanks and attack helicopters. This dissertation describes the research needed to demonstrate both the feasibility and utility of the API. Part of the research describes implementation of a silicon focal plane array (SFPA) capable of both active and passive imaging. The passive imaging mode exceeds the nighttime performance of currently fielded, man-portable sensors. Further, when scene illumination is insufficient for passive imaging, the low dark current of SFPA makes it possible to use continuous wave laser diodes (CWLD) to add an active imaging mode. CWLD have advantages of size, efficiency, and improved eye safety when compared to high peak-power diodes. Because of the improved eye safety, the API provides user-demanded features like video output and extended range gates in the active as well as passive imaging modes. Like any other night vision device, the API depends on natural illumination of the scene for passive operation. Although it has been known for decades that "starlight" illumination is actually from diffuse airglow emissions, the research described in this dissertation provides the first estimates of the global and temporal variation of ground illumination due to airglow. A third related element of the current research establishes the impact of atmospheric aerosols on API performance. We know from day experience that atmospheric scattering of sunlight into the imager line-of-sight can blind the imager and drastically degrade performance. Atmospheric scattering of sunlight is extensively covered in the literature. However, previous literature did not cover the impact of atmospheric scattering when the target is diffusely illuminated by airglow.

Molecular characterization of Api g 2, a novel allergenic member of the lipid-transfer protein 1 family from celery stalks.

PubMed

Gadermaier, Gabriele; Egger, Matthias; Girbl, Tamara; Erler, Anja; Harrer, Andrea; Vejvar, Eva; Liso, Marina; Richter, Klaus; Zuidmeer, Laurian; Mari, Adriano; Ferreira, Fatima

2011-04-01

Celery represents a relevant cross-reactive food allergen source in the adult population. As the currently known allergens are not typical elicitors of severe symptoms, we aimed to identify and characterize a non-specific lipid transfer protein (nsLTP). MS and cDNA cloning were applied to obtain the full-length sequence of a novel allergenic nsLTP from celery stalks. The purified natural molecule consisted of a single isoallergen designated as Api g 2.0101, which was recombinantly produced in Escherichia coli Rosetta-gami. The natural and recombinant molecules displayed equivalent physicochemical and immunological properties. Circular dichroism revealed a typical α-helical fold and high thermal stability. Moreover, Api g 2 was highly resistant to simulated gastrointestinal digestion. As assessed by ELISA, thermal denaturation did not affect the IgE binding of Api g 2. Natural and recombinant Api g 2 showed similar allergenic activity in mediator release assays. Api g 2-specific IgE antibodies cross-reacted with peach and mugwort pollen nsLTPs. Based on our results, it can be anticipated that inclusion of recombinant Api g 2 in the current panel of allergens for molecule-based diagnosis will facilitate the evaluation of the clinical relevance of nsLTP sensitization in celery allergy and help clinicians in the management of food allergic patients. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

JEnsembl: a version-aware Java API to Ensembl data systems

PubMed Central

Paterson, Trevor; Law, Andy

2012-01-01

Motivation: The Ensembl Project provides release-specific Perl APIs for efficient high-level programmatic access to data stored in various Ensembl database schema. Although Perl scripts are perfectly suited for processing large volumes of text-based data, Perl is not ideal for developing large-scale software applications nor embedding in graphical interfaces. The provision of a novel Java API would facilitate type-safe, modular, object-orientated development of new Bioinformatics tools with which to access, analyse and visualize Ensembl data. Results: The JEnsembl API implementation provides basic data retrieval and manipulation functionality from the Core, Compara and Variation databases for all species in Ensembl and EnsemblGenomes and is a platform for the development of a richer API to Ensembl datasources. The JEnsembl architecture uses a text-based configuration module to provide evolving, versioned mappings from database schema to code objects. A single installation of the JEnsembl API can therefore simultaneously and transparently connect to current and previous database instances (such as those in the public archive) thus facilitating better analysis repeatability and allowing ‘through time’ comparative analyses to be performed. Availability: Project development, released code libraries, Maven repository and documentation are hosted at SourceForge (http://jensembl.sourceforge.net). Contact: jensembl-develop@lists.sf.net, andy.law@roslin.ed.ac.uk, trevor.paterson@roslin.ed.ac.uk PMID:22945789

Prioritization of pharmaceuticals based on risks to aquatic environments in Kazakhstan.

PubMed

Aubakirova, Bakhyt; Beisenova, Raikhan; Boxall, Alistair Ba

2017-09-01

Over the last 20 years, there has been increasing interest in the occurrence, fate, effects, and risk of pharmaceuticals in the natural environment. However, we still have only limited or no data on ecotoxicological risks of many of the active pharmaceutical ingredients (APIs) currently in use. This is partly due to the fact that the environmental assessment of an API is an expensive, time-consuming, and complicated process. Prioritization methodologies, which aim to identify APIs of most concern in a particular situation, could therefore be invaluable in focusing experimental work on APIs that really matter. The majority of approaches for prioritizing APIs require annual pharmaceutical usage data. These methods cannot therefore be applied to countries, such as Kazakhstan, that have very limited data on API usage. The present paper therefore offers an approach for prioritizing APIs in surface waters in information-poor regions such as Kazakhstan. Initially data were collected on the number of products and active ingredients for different therapeutic classes in use in Kazakhstan and on the typical doses. These data were then used alongside simple exposure modeling approaches to estimate exposure indices for active ingredients (about 240 APIs) in surface waters in the country. Ecotoxicological effects data were obtained from the literature or predicted. Risk quotients were then calculated for each pharmaceutical based on the exposure and the substances were ranked in order of risk quotient. Highest exposure indices were obtained for benzylpenicillin, metronidazole, sulbactam, ceftriaxone, and sulfamethoxazole. The highest risk was estimated for amoxicillin, clarithromycin, azithromycin, ketoconazole, and benzylpenicillin. In the future, the approach could be employed in other regions where usage information is limited. Integr Environ Assess Manag 2017;13:832-839. © 2017 SETAC. © 2017 SETAC.

Addressing the diversity of the honeybee gut symbiont Gilliamella: description of Gilliamella apis sp. nov., isolated from the gut of honeybees (Apis mellifera).

PubMed

Ludvigsen, Jane; Porcellato, Davide; Amdam, Gro V; Rudi, Knut

2018-05-01

The gut microbiota of honeybees (Apis) and bumblebees (Bombus) include the symbiotic bacterial genus Gilliamella. This genus shows a high degree of functional and genomic diversity and separates into distinct lineages. Gilliamella apicola wkB1 T , which was isolated from Apis, was the first species to be described. Recently four new species, isolated from Bombus, were identified. In this paper, we compare several genomes/strains from previous studies spanning this diversity, which gives insight into the phylogenetic relationship among different Gilliamella species. We show that one lineage, isolated only from Apis, is different from other gilliamellas described, based on average nucleotide identity calculation (about 80 %) and phenotypic characterizations. We propose the new species name for this lineage: Gilliamella apis sp. nov. We present the characterization of the type strain NO3 T (=DSM 105629 T =LMG 30293 T ), a strain isolated from the Western honeybee Apis mellifera, which clusters within this lineage. Cells of strain NO3 T grow best in a microaerophilic atmosphere with enhanced CO2 levels at 36 °C and pH 7.0-7.5. Cells also grow well in anaerobic conditions, but not in aerobic conditions. Cells are approximately 1 µm in length and rod-shaped, and the genomic G+C content is 34.7 mol%. Differential characteristics between strain NO3 T and the different type strains of Gilliamella were revealed based on API kit tests and genomic content comparisons. The main respiratory quinone of strain NO3 T was ubiquinone-8, and the predominant fatty acids were C18 : 1ω7c/C18 : 1ω6c, C16 : 0, consistent with the genus Gilliamella.

Use of an innovative T-tube maze assay and the proboscis extension response assay to assess sublethal effects of GM products and pesticides on learning capacity of the honey bee Apis mellifera L.

PubMed

Han, Peng; Niu, Chang-Ying; Lei, Chao-Liang; Cui, Jin-Jie; Desneux, Nicolas

2010-11-01

Transgenic Cry1Ac+CpTI cotton (CCRI41) is a promising cotton cultivar throughout China but side effects and especially sublethal effects of this transgenic cultivar on beneficial insects remain poorly studied. More specifically potential sublethal effects on behavioural traits of the honey bee Apis mellifera L. have not been formally assessed despite the importance of honey bees for pollination. The goal of our study was to assess potential effects of CCRI41 cotton pollen on visual and olfactory learning by honey bees. After a 7-day oral chronic exposure to honey mixed with either CCRI41 pollen, imidacloprid-treated conventional pollen (used as positive sublethal control) or conventional pollen (control), learning performance was evaluated by the classical proboscis extension reflex (PER) procedure as well as a T-tube maze test. The latter assay was designed as a new device to assess potential side effects of pesticides on visual associative learning of honey bees. These two procedures were complementary because the former focused on olfactory learning while the latter was involved in visual learning based on visual orientation ability. Oral exposure to CCRI41 pollen did not affect learning capacities of honey bees in both the T-tube maze and PER tests. However, exposure to imidacloprid resulted in reduced visual learning capacities in T-tube maze evaluation and decreased olfactory learning performances measured with PER. The implications of these results are discussed in terms of risks of transgenic CCRI41 cotton crops for honey bees.

New solid-state chemistry technologies to bring better drugs to market: knowledge-based decision making.

PubMed

Park, Aeri; Chyall, Leonard J; Dunlap, Jeanette; Schertz, Christine; Jonaitis, David; Stahly, Barbara C; Bates, Simon; Shipplett, Rex; Childs, Scott

2007-01-01

Modern drug development demands constant deployment of more effective technologies to mitigate the high cost of bringing new drugs to market. In addition to cost savings, new technologies can improve all aspects of pharmaceutical development. New technologies developed at SSCI, Inc. include solid form development of an active pharmaceutical ingredients. (APIs) are PatternMatch software and capillary-based crystallisation techniques that not only allow for fast and effective solid form screening, but also extract maximum property information from the routine screening data that is generally available. These new technologies offer knowledge-based decision making during solid form development of APIs and result in more developable API solid forms.

Investigation into process-induced de-aggregation of cohesive micronised API particles.

PubMed

Hoffmann, Magnus; Wray, Patrick S; Gamble, John F; Tobyn, Mike

2015-09-30

The aim of this study was to assess the impact of unit processes on the de-aggregation of a cohesive micronised API within a pharmaceutical formulation using near-infrared chemical imaging. The impact on the primary API particles was also investigated using an image-based particle characterization system with integrated Raman analysis. The blended material was shown to contain large, API rich domains which were distributed in-homogeneously across the sample, suggesting that the blending process was not aggressive enough to disperse aggregates of micronised drug particles. Cone milling, routinely used to improve the homogeneity of such cohesive formulations, was observed to substantially reduce the number and size of API rich domains; however, several smaller API domains survived the milling process. Conveyance of the cone milled formulation through the Alexanderwerk WP120 powder feed system completely dispersed all remaining aggregates. Importantly, powder feed transmission of the un-milled formulation was observed to produce an equally homogeneous API distribution. The size of the micronised primary drug particles remained unchanged during powder feed transmission. These findings provide further evidence that this powder feed system does induce shear, and is in fact better able to disperse aggregates of a cohesive micronised API within a blend than the blend-mill-blend step. Crown Copyright © 2015. Published by Elsevier B.V. All rights reserved.

Apoptosis inhibitor 5 (API-5; AAC-11; FIF) is upregulated in human carcinomas in vivo.

PubMed

Koci, Lenka; Chlebova, Katarina; Hyzdalova, Martina; Hofmanova, Jirina; Jira, Miroslav; Kysela, Petr; Kozubik, Alois; Kala, Zdenek; Krejci, Pavel

2012-04-01

Apoptosis inhibitor 5 (API-5) is a 55 kDa nuclear protein with potent anti-apoptotic signaling in tumor cells in vitro. In this study, we analyzed the expression of the API-5 protein in vivo in a broad spectrum of human carcinomas, including those of the colon, lung, liver, kidney, pancreas, stomach and esophagus using tumor tissues obtained during tumor resection. The results showed significant upregulation of API-5 expression in biopsies of lung (23%, n=13) and colorectal tumors (33%, n=27) in comparison with biopsies from the adjacent normal tissue. Colon cancer biopsies were used to study the cell populations with an upregulated level of expression of API-5 more closely. Using a magnetic bead-based selection for the epithelial cell marker EpCAM, we purified epithelial cells from the tumor and control tissues and analyzed these cells for API-5 expression by western immunoblotting. We observed that EpCAM-positive tumor cells expressed API-5 in all three colorectal cancer cases tested, in contrast to the control EpCAM-positive and EpCAM-negative cells isolated from the control or tumor tissues. These data suggest that the expression of the API-5 protein is upregulated in tumor epithelial cells and may serve as a prognostic marker in colorectal cancer.

The M358R variant of α{sub 1}-proteinase inhibitor inhibits coagulation factor VIIa

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

Sheffield, William P., E-mail: sheffiel@mcmaster.ca; Department of Pathology and Molecular Medicine, McMaster University, Hamilton, Ontario; Bhakta, Varsha

The naturally occurring M358R mutation of the plasma serpin α{sub 1}-proteinase inhibitor (API) changes both its cleavable reactive centre bond to Arg–Ser and the efficacy with which it inhibits different proteases, reducing the rate of inhibition of neutrophil elastase, and enhancing that of thrombin, factor XIa, and kallikrein, by several orders of magnitude. Although another plasma serpin with an Arg–Ser reactive centre, antithrombin (AT), has been shown to inhibit factor VIIa (FVIIa), no published data are available with respect to FVIIa inhibition by API M358R. Recombinant bacterially-expressed API M358R and plasma-derived AT were therefore compared using gel-based and kinetic assaysmore » of FVIIa integrity and activity. Under pseudo-first order conditions of excess serpin over protease, both AT and API M358R formed denaturation-resistant inhibitory complexes with FVIIa in reactions accelerated by TF; AT, but not API M358R, also required heparin for maximal activity. The second order rate constant for heparin-independent API M358R-mediated FVIIa inhibition was determined to be 7.8 ± 0.8 × 10{sup 2} M{sup −1}sec{sup −1}. We conclude that API M358R inhibits FVIIa by forming inhibitory complexes of the serpin type more rapidly than AT in the absence of heparin. The likely 20-fold excess of API M358R over AT in patient plasma during inflammation raises the possibility that it could contribute to the hemorrhagic tendencies manifested by rare individuals expressing this mutant serpin. - Highlights: • The inhibitory specificity of the serpin alpha-1-proteinase inhibitor (API) is sharply altered in the M358R variant. • API M358R forms denaturation-resistant complexes with coagulation factor VIIa at a rate accelerated by tissue factor but unaffected by heparin. • Complex formation was shown by gel-based assays and quantified kinetically by inhibition of FVIIa-dependent amidolysis.« less

A knowledge discovery object model API for Java

PubMed Central

Zuyderduyn, Scott D; Jones, Steven JM

2003-01-01

Background Biological data resources have become heterogeneous and derive from multiple sources. This introduces challenges in the management and utilization of this data in software development. Although efforts are underway to create a standard format for the transmission and storage of biological data, this objective has yet to be fully realized. Results This work describes an application programming interface (API) that provides a framework for developing an effective biological knowledge ontology for Java-based software projects. The API provides a robust framework for the data acquisition and management needs of an ontology implementation. In addition, the API contains classes to assist in creating GUIs to represent this data visually. Conclusions The Knowledge Discovery Object Model (KDOM) API is particularly useful for medium to large applications, or for a number of smaller software projects with common characteristics or objectives. KDOM can be coupled effectively with other biologically relevant APIs and classes. Source code, libraries, documentation and examples are available at . PMID:14583100

Engineered particles demonstrate improved flow properties at elevated drug loadings for direct compression manufacturing.

PubMed

Trementozzi, Andrea N; Leung, Cheuk-Yui; Osei-Yeboah, Frederick; Irdam, Erwin; Lin, Yiqing; MacPhee, J Michael; Boulas, Pierre; Karki, Shyam B; Zawaneh, Peter N

2017-05-15

Optimizing powder flow and compaction properties are critical for ensuring a robust tablet manufacturing process. The impact of flow and compaction properties of the active pharmaceutical ingredient (API) becomes progressively significant for higher drug load formulations, and for scaling up manufacturing processes. This study demonstrated that flow properties of a powder blend can be improved through API particle engineering, without critically impacting blend tabletability at elevated drug loadings. In studying a jet milled API (D 50 =24μm) and particle engineered wet milled API (D 50 =70μm and 90μm), flow functions of all API lots were similarly poor despite the vast difference in average particle size (ff c <4). This finding strays from the common notion that powder flow properties are directly correlated to particle size distribution. Upon adding excipients, however, clear trends in flow functions based on API particle size were observed. Wet milled API blends had a much improved flow function (ff c >10) compared with the jet milled API blends. Investigation of the compaction properties of both wet and jet milled powder blends also revealed that both jet and wet milled material produced robust tablets at the drug loadings used. The ability to practically demonstrate this uncommon observation that similarly poor flowing APIs can lead to a marked difference upon blending is important for pharmaceutical development. It is especially important in early phase development during API selection, and is advantageous particularly when material-sparing techniques are utilized. Copyright © 2017 Elsevier B.V. All rights reserved.

The JANA calibrations and conditions database API

NASA Astrophysics Data System (ADS)

Lawrence, David

2010-04-01

Calibrations and conditions databases can be accessed from within the JANA Event Processing framework through the API defined in its JCalibration base class. The API is designed to support everything from databases, to web services to flat files for the backend. A Web Service backend using the gSOAP toolkit has been implemented which is particularly interesting since it addresses many modern cybersecurity issues including support for SSL. The API allows constants to be retrieved through a single line of C++ code with most of the context, including the transport mechanism, being implied by the run currently being analyzed and the environment relieving developers from implementing such details.

Component resolution reveals additional major allergens in patients with honeybee venom allergy.

PubMed

Köhler, Julian; Blank, Simon; Müller, Sabine; Bantleon, Frank; Frick, Marcel; Huss-Marp, Johannes; Lidholm, Jonas; Spillner, Edzard; Jakob, Thilo

2014-05-01

Detection of IgE to recombinant Hymenoptera venom allergens has been suggested to improve the diagnostic precision in Hymenoptera venom allergy. However, the frequency of sensitization to the only available recombinant honeybee venom (HBV) allergen, rApi m 1, in patients with HBV allergy is limited, suggesting that additional HBV allergens might be of relevance. We performed an analysis of sensitization profiles of patients with HBV allergy to a panel of HBV allergens. Diagnosis of HBV allergy (n = 144) was based on history, skin test results, and allergen-specific IgE levels to HBV. IgE reactivity to 6 HBV allergens devoid of cross-reactive carbohydrate determinants (CCD) was analyzed by ImmunoCAP. IgE reactivity to rApi m 1, rApi m 2, rApi m 3, nApi m 4, rApi m 5, and rApi m 10 was detected in 72.2%, 47.9%, 50.0%, 22.9%, 58.3%, and 61.8% of the patients with HBV allergy, respectively. Positive results to at least 1 HBV allergen were detected in 94.4%. IgE reactivity to Api m 3, Api m 10, or both was detected in 68.0% and represented the only HBV allergen-specific IgE in 5% of the patients. Limited inhibition of IgE binding by therapeutic HBV and limited induction of Api m 3- and Api m 10-specific IgG4 in patients obtaining immunotherapy supports recent reports on the underrepresentation of these allergens in therapeutic HBV preparations. Analysis of a panel of CCD-free HBV allergens improved diagnostic sensitivity compared with use of rApi m 1 alone, identified additional major allergens, and revealed sensitizations to allergens that have been reported to be absent or underrepresented in therapeutic HBV preparations. Copyright © 2014 The Authors. Published by Mosby, Inc. All rights reserved.

Collaborative development of predictive toxicology applications

PubMed Central

2010-01-01

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals. The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation. Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way. PMID:20807436

Collaborative development of predictive toxicology applications.

PubMed

Hardy, Barry; Douglas, Nicki; Helma, Christoph; Rautenberg, Micha; Jeliazkova, Nina; Jeliazkov, Vedrin; Nikolova, Ivelina; Benigni, Romualdo; Tcheremenskaia, Olga; Kramer, Stefan; Girschick, Tobias; Buchwald, Fabian; Wicker, Joerg; Karwath, Andreas; Gütlein, Martin; Maunz, Andreas; Sarimveis, Haralambos; Melagraki, Georgia; Afantitis, Antreas; Sopasakis, Pantelis; Gallagher, David; Poroikov, Vladimir; Filimonov, Dmitry; Zakharov, Alexey; Lagunin, Alexey; Gloriozova, Tatyana; Novikov, Sergey; Skvortsova, Natalia; Druzhilovsky, Dmitry; Chawla, Sunil; Ghosh, Indira; Ray, Surajit; Patel, Hitesh; Escher, Sylvia

2010-08-31

OpenTox provides an interoperable, standards-based Framework for the support of predictive toxicology data management, algorithms, modelling, validation and reporting. It is relevant to satisfying the chemical safety assessment requirements of the REACH legislation as it supports access to experimental data, (Quantitative) Structure-Activity Relationship models, and toxicological information through an integrating platform that adheres to regulatory requirements and OECD validation principles. Initial research defined the essential components of the Framework including the approach to data access, schema and management, use of controlled vocabularies and ontologies, architecture, web service and communications protocols, and selection and integration of algorithms for predictive modelling. OpenTox provides end-user oriented tools to non-computational specialists, risk assessors, and toxicological experts in addition to Application Programming Interfaces (APIs) for developers of new applications. OpenTox actively supports public standards for data representation, interfaces, vocabularies and ontologies, Open Source approaches to core platform components, and community-based collaboration approaches, so as to progress system interoperability goals.The OpenTox Framework includes APIs and services for compounds, datasets, features, algorithms, models, ontologies, tasks, validation, and reporting which may be combined into multiple applications satisfying a variety of different user needs. OpenTox applications are based on a set of distributed, interoperable OpenTox API-compliant REST web services. The OpenTox approach to ontology allows for efficient mapping of complementary data coming from different datasets into a unifying structure having a shared terminology and representation.Two initial OpenTox applications are presented as an illustration of the potential impact of OpenTox for high-quality and consistent structure-activity relationship modelling of REACH-relevant endpoints: ToxPredict which predicts and reports on toxicities for endpoints for an input chemical structure, and ToxCreate which builds and validates a predictive toxicity model based on an input toxicology dataset. Because of the extensible nature of the standardised Framework design, barriers of interoperability between applications and content are removed, as the user may combine data, models and validation from multiple sources in a dependable and time-effective way.

Extending Climate Analytics-As to the Earth System Grid Federation

NASA Astrophysics Data System (ADS)

Tamkin, G.; Schnase, J. L.; Duffy, D.; McInerney, M.; Nadeau, D.; Li, J.; Strong, S.; Thompson, J. H.

2015-12-01

We are building three extensions to prior-funded work on climate analytics-as-a-service that will benefit the Earth System Grid Federation (ESGF) as it addresses the Big Data challenges of future climate research: (1) We are creating a cloud-based, high-performance Virtual Real-Time Analytics Testbed supporting a select set of climate variables from six major reanalysis data sets. This near real-time capability will enable advanced technologies like the Cloudera Impala-based Structured Query Language (SQL) query capabilities and Hadoop-based MapReduce analytics over native NetCDF files while providing a platform for community experimentation with emerging analytic technologies. (2) We are building a full-featured Reanalysis Ensemble Service comprising monthly means data from six reanalysis data sets. The service will provide a basic set of commonly used operations over the reanalysis collections. The operations will be made accessible through NASA's climate data analytics Web services and our client-side Climate Data Services (CDS) API. (3) We are establishing an Open Geospatial Consortium (OGC) WPS-compliant Web service interface to our climate data analytics service that will enable greater interoperability with next-generation ESGF capabilities. The CDS API will be extended to accommodate the new WPS Web service endpoints as well as ESGF's Web service endpoints. These activities address some of the most important technical challenges for server-side analytics and support the research community's requirements for improved interoperability and improved access to reanalysis data.

Influence of humidity on the phase behavior of API/polymer formulations.

PubMed

Prudic, Anke; Ji, Yuanhui; Luebbert, Christian; Sadowski, Gabriele

2015-08-01

Amorphous formulations of APIs in polymers tend to absorb water from the atmosphere. This absorption of water can induce API recrystallization, leading to reduced long-term stability during storage. In this work, the phase behavior of different formulations was investigated as a function of relative humidity. Indomethacin and naproxen were chosen as model APIs and poly(vinyl pyrrolidone) (PVP) and poly(vinyl pyrrolidone-co-vinyl acetate) (PVPVA64) as excipients. The formulations were prepared by spray drying. The water sorption in pure polymers and in formulations was measured at 25°C and at different values of relative humidity (RH=25%, 50% and 75%). Most water was absorbed in PVP-containing systems, and water sorption was decreasing with increasing API content. These trends could also be predicted in good agreement with the experimental data using the thermodynamic model PC-SAFT. Furthermore, the effect of absorbed water on API solubility in the polymer and on the glass-transition temperature of the formulations was predicted with PC-SAFT and the Gordon-Taylor equation, respectively. The absorbed water was found to significantly decrease the API solubility in the polymer as well as the glass-transition temperature of the formulation. Based on a quantitative modeling of the API/polymer phase diagrams as a function of relative humidity, appropriate API/polymer compositions can now be selected to ensure long-term stable amorphous formulations at given storage conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

Towards integrated drug substance and drug product design for an active pharmaceutical ingredient using particle engineering.

PubMed

Kougoulos, Eleftherios; Smales, Ian; Verrier, Hugh M

2011-03-01

A novel experimental approach describing the integration of drug substance and drug production design using particle engineering techniques such as sonocrystallization, high shear wet milling (HSWM) and dry impact (hammer) milling were used to manufacture samples of an active pharmaceutical ingredient (API) with diverse particle size and size distributions. The API instability was addressed using particle engineering and through judicious selection of excipients to reduce degradation reactions. API produced using a conventional batch cooling crystallization process resulted in content uniformity issues. Hammer milling increased fine particle formation resulting in reduced content uniformity and increased degradation compared to sonocrystallized and HSWM API in the formulation. To ensure at least a 2-year shelf life based on predictions using an Accelerated Stability Assessment Program, this API should have a D [v, 0.1] of 55 μm and a D [v, 0.5] of 140 μm. The particle size of the chief excipient in the drug product formulation needed to be close to that of the API to avoid content uniformity and stability issues but large enough to reduce lactam formation. The novel methodology described here has potential for application to other APIs. © 2011 American Association of Pharmaceutical Scientists

Solid-state NMR studies of form I of atorvastatin calcium.

PubMed

Wang, Wei David; Gao, Xudong; Strohmeier, Mark; Wang, Wei; Bai, Shi; Dybowski, Cecil

2012-03-22

Solid-state (13)C, (19)F, and (15)N magic angle spinning NMR studies of Form I of atorvastatin calcium are reported, including chemical shift tensors of all resolvable carbon sites and fluorine sites. The complete (13)C and (19)F chemical shift assignments are given based on an extensive analysis of (13)C-(1)H HETCOR and (13)C-(19)F HETCOR results. The solid-state NMR data indicate that the asymmetric unit of this material contains two atorvastatin molecules. A possible structure of Form I of atorvastatin calcium (ATC-I), derived from solid-state NMR data and density functional theory calculations of various structures, is proposed for this important active pharmaceutical ingredient (API).

Migrating Department of Defense (DoD) Web Service Based Applications to Mobile Computing Platforms

DTIC Science & Technology

2012-03-01

World Wide Web Consortium (W3C) Geolocation API to identify the device’s location and then center the map on the device. Finally, we modify the entry...THIS PAGE INTENTIONALLY LEFT BLANK xii List of Acronyms and Abbreviations API Application Programming Interface CSS Cascading Style Sheets CLIMO...Java API for XML Web Services Reference Implementation JS JavaScript JSNI JavaScript Native Interface METOC Meteorological and Oceanographic MAA Mobile

Apigenin enhances the antitumor effects of cetuximab in nasopharyngeal carcinoma by inhibiting EGFR signaling.

PubMed

Hu, Wen-Jian; Liu, Jing; Zhong, Lun-Kun; Wang, Jian

2018-06-01

Nasopharyngeal carcinoma (NPC) is a type of head and neck cancers with poor prognosis. Despite that platinum-based chemotherapy concurrent with radiotherapy have made great achievements for the treatment of NPC, the therapeutic reaction and toxicity varies dramatically among individuals. Apigenin (API), a naturally occurring plant flavone, is considered to have anti-cancer effect. Cetuximab (CET), a well known epidermal growth factor receptor (EGFR) inhibitor, is widely used in various cancers, especially head and neck cancers. The aim of our study was to measure the combination of API and CET for the treatment of NPC in vitro and in vivo. Results demonstrated that combining API and CET could better suppress the viability of the human nasopharyngeal carcinoma cell lines (HONE1 and CNE2) and inhibit the growth of NPC than API or CET used alone. Besides, the combination of API with CET produced greater pro-apoptosis effect. Moreover, the increased G2/M phase arrest caused by CET could be remarkably enhanced by adding API in HONE1 and CNE2 cells. Although, both API and CET could decrease the expressions of p-EGFR, p-Akt, p-STAT3 and Cyclin D1. Combining them produced greater inhibition effect. These results suggested that the combination of API and CET may be a promising therapeutic approach for the treatment of NPC. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

An Application Programming Interface for Synthetic Snowflake Particle Structure and Scattering Data

NASA Technical Reports Server (NTRS)

Lammers, Matthew; Kuo, Kwo-Sen

2017-01-01

The work by Kuo and colleagues on growing synthetic snowflakes and calculating their single-scattering properties has demonstrated great potential to improve the retrievals of snowfall. To grant colleagues flexible and targeted access to their large collection of sizes and shapes at fifteen (15) microwave frequencies, we have developed a web-based Application Programming Interface (API) integrated with NASA Goddard's Precipitation Processing System (PPS) Group. It is our hope that the API will enable convenient programmatic utilization of the database. To help users better understand the API's capabilities, we have developed an interactive web interface called the OpenSSP API Query Builder, which implements an intuitive system of mechanisms for selecting shapes, sizes, and frequencies to generate queries, with which the API can then extract and return data from the database. The Query Builder also allows for the specification of normalized particle size distributions by setting pertinent parameters, with which the API can also return mean geometric and scattering properties for each size bin. Additionally, the Query Builder interface enables downloading of raw scattering and particle structure data packages. This presentation will describe some of the challenges and successes associated with developing such an API. Examples of its usage will be shown both through downloading output and pulling it into a spreadsheet, as well as querying the API programmatically and working with the output in code.

DAX - The Next Generation: Towards One Million Processes on Commodity Hardware.

PubMed

Damon, Stephen M; Boyd, Brian D; Plassard, Andrew J; Taylor, Warren; Landman, Bennett A

2017-01-01

Large scale image processing demands a standardized way of not only storage but also a method for job distribution and scheduling. The eXtensible Neuroimaging Archive Toolkit (XNAT) is one of several platforms that seeks to solve the storage issues. Distributed Automation for XNAT (DAX) is a job control and distribution manager. Recent massive data projects have revealed several bottlenecks for projects with >100,000 assessors (i.e., data processing pipelines in XNAT). In order to address these concerns, we have developed a new API, which exposes a direct connection to the database rather than REST API calls to accomplish the generation of assessors. This method, consistent with XNAT, keeps a full history for auditing purposes. Additionally, we have optimized DAX to keep track of processing status on disk (called DISKQ) rather than on XNAT, which greatly reduces load on XNAT by vastly dropping the number of API calls. Finally, we have integrated DAX into a Docker container with the idea of using it as a Docker controller to launch Docker containers of image processing pipelines. Using our new API, we reduced the time to create 1,000 assessors (a sub-cohort of our case project) from 65040 seconds to 229 seconds (a decrease of over 270 fold). DISKQ, using pyXnat, allows launching of 400 jobs in under 10 seconds which previously took 2,000 seconds. Together these updates position DAX to support projects with hundreds of thousands of scans and to run them in a time-efficient manner.

DAX - the next generation: towards one million processes on commodity hardware

NASA Astrophysics Data System (ADS)

Damon, Stephen M.; Boyd, Brian D.; Plassard, Andrew J.; Taylor, Warren; Landman, Bennett A.

2017-03-01

Large scale image processing demands a standardized way of not only storage but also a method for job distribution and scheduling. The eXtensible Neuroimaging Archive Toolkit (XNAT) is one of several platforms that seeks to solve the storage issues. Distributed Automation for XNAT (DAX) is a job control and distribution manager. Recent massive data projects have revealed several bottlenecks for projects with <100,000 assessors (i.e., data processing pipelines in XNAT). In order to address these concerns, we have developed a new API, which exposes a direct connection to the database rather than REST API calls to accomplish the generation of assessors. This method, consistent with XNAT, keeps a full history for auditing purposes. Additionally, we have optimized DAX to keep track of processing status on disk (called DISKQ) rather than on XNAT, which greatly reduces load on XNAT by vastly dropping the number of API calls. Finally, we have integrated DAX into a Docker container with the idea of using it as a Docker controller to launch Docker containers of image processing pipelines. Using our new API, we reduced the time to create 1,000 assessors (a sub-cohort of our case project) from 65040 seconds to 229 seconds (a decrease of over 270 fold). DISKQ, using pyXnat, allows launching of 400 jobs in under 10 seconds which previously took 2,000 seconds. Together these updates position DAX to support projects with hundreds of thousands of scans and to run them in a time-efficient manner.

DAX - The Next Generation: Towards One Million Processes on Commodity Hardware

PubMed Central

Boyd, Brian D.; Plassard, Andrew J.; Taylor, Warren; Landman, Bennett A.

2017-01-01

Large scale image processing demands a standardized way of not only storage but also a method for job distribution and scheduling. The eXtensible Neuroimaging Archive Toolkit (XNAT) is one of several platforms that seeks to solve the storage issues. Distributed Automation for XNAT (DAX) is a job control and distribution manager. Recent massive data projects have revealed several bottlenecks for projects with >100,000 assessors (i.e., data processing pipelines in XNAT). In order to address these concerns, we have developed a new API, which exposes a direct connection to the database rather than REST API calls to accomplish the generation of assessors. This method, consistent with XNAT, keeps a full history for auditing purposes. Additionally, we have optimized DAX to keep track of processing status on disk (called DISKQ) rather than on XNAT, which greatly reduces load on XNAT by vastly dropping the number of API calls. Finally, we have integrated DAX into a Docker container with the idea of using it as a Docker controller to launch Docker containers of image processing pipelines. Using our new API, we reduced the time to create 1,000 assessors (a sub-cohort of our case project) from 65040 seconds to 229 seconds (a decrease of over 270 fold). DISKQ, using pyXnat, allows launching of 400 jobs in under 10 seconds which previously took 2,000 seconds. Together these updates position DAX to support projects with hundreds of thousands of scans and to run them in a time-efficient manner. PMID:28919661

In Vivo Efficacy and Pharmacokinetics of Optimized Apidaecin Analogs

NASA Astrophysics Data System (ADS)

Schmidt, Rico; Knappe, Daniel; Wende, Elisabeth; Ostorházi, Eszter; Hoffmann, Ralf

2017-03-01

Proline-rich antimicrobial peptides (PrAMPs) represent promising alternative therapeutic options for the treatment of multidrug-resistant bacterial infections. PrAMPs are predominantly active against Gram-negative bacteria by inhibiting protein expression via at least two different modes of action, i.e., blocking the ribosomal exit tunnel of 70S ribosomes (oncocin-type binding) or inhibiting the assembly of the 50S ribosomal subunit (apidaecin-type binding). The in vivo efficacy and favorable biodistribution of oncocins confirmed the therapeutic potential of short PrAMPs for the first time, whereas the in vivo evaluation of apidaecins is still limited despite the promising efficacy of apidaecin-analog Api88 in an intraperitoneal murine infection model. Here, the in vivo efficacy of apidaecin-analog Api137 was studied, which rescued all NMRI mice from a lethal intraperitoneal infection with E. coli ATCC 25922 when administered three times intraperitoneal at doses of 0.6 mg/kg starting one hour after infection. When Api88 and Api137 were administered intravenous or intraperitoneal at doses of 5 and 20 mg/kg, their plasma levels were similarly low (<3 µg/mL) and fourfold lower than for oncocin-analog Onc72. This contradicted earlier expectation based on the very low serum stability of Api88 with a half-life time of only 5 min compared to 6 hrs and 3 hrs for Api137 and Onc72, respectively. Pharmacokinetic data relying on a sensitive mass spectrometry method utilizing multiple reaction monitoring and isotope-labeled peptides revealed that Api88 and Api137 were present in blood, urine, and kidney, and liver homogenates at similar levels accompanied by the same major metabolites comprising residues 1-16 and 1-17. The pretended discrepancy was solved, when all peptides were incubated in peritoneal lavage. Api137 was rapidly degraded at the C-terminus, while Api88 was rather stable despite releasing the same degradation products. Onc72 was very stable explaining its higher plasma levels compared to Api88 and Api137 after intraperitoneal administration illuminating its good in vivo efficacy. The data indicate that the degradation of therapeutic peptides should be studied in serum and further body fluids. Moreover, the high efficacy in murine infection models and the fast clearance of Api88 and Api137 within 60 min after intravenous and 90 min after intraperitoneal injections indicate that

Yoink: An interaction-based partitioning API.

PubMed

Zheng, Min; Waller, Mark P

2018-05-15

Herein, we describe the implementation details of our interaction-based partitioning API (application programming interface) called Yoink for QM/MM modeling and fragment-based quantum chemistry studies. Interactions are detected by computing density descriptors such as reduced density gradient, density overlap regions indicator, and single exponential decay detector. Only molecules having an interaction with a user-definable QM core are added to the QM region of a hybrid QM/MM calculation. Moreover, a set of molecule pairs having density-based interactions within a molecular system can be computed in Yoink, and an interaction graph can then be constructed. Standard graph clustering methods can then be applied to construct fragments for further quantum chemical calculations. The Yoink API is licensed under Apache 2.0 and can be accessed via yoink.wallerlab.org. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Layered approach to workstation design for medical image viewing

NASA Astrophysics Data System (ADS)

Haynor, David R.; Zick, Gregory L.; Heritage, Marcus B.; Kim, Yongmin

1992-07-01

Software engineering principles suggest that complex software systems are best constructed from independent, self-contained modules, thereby maximizing the portability, maintainability and modifiability of the produced code. This principal is important in the design of medical imaging workstations, where further developments in technology (CPU, memory, interface devices, displays, network connections) are required for clinically acceptable workstations, and it is desirable to provide different hardware platforms with the ''same look and feel'' for the user. In addition, the set of desired functions is relatively well understood, but the optimal user interface for delivering these functions on a clinically acceptable workstation is still different depending on department, specialty, or individual preference. At the University of Washington, we are developing a viewing station based on the IBM RISC/6000 computer and on new technologies that are just becoming commercially available. These include advanced voice recognition systems and an ultra-high-speed network. We are developing a set of specifications and a conceptual design for the workstation, and will be producing a prototype. This paper presents our current concepts concerning the architecture and software system design of the future prototype. Our conceptual design specifies requirements for a Database Application Programming Interface (DBAPI) and for a User API (UAPI). The DBAPI consists of a set of subroutine calls that define the admissible transactions between the workstation and an image archive. The UAPI describes the requests a user interface program can make of the workstation. It incorporates basic display and image processing functions, yet is specifically designed to allow extensions to the basic set at the application level. We will discuss the fundamental elements of the two API''s and illustrate their application to workstation design.

Helioviewer.org: Simple Solar and Heliospheric Data Visualization

NASA Astrophysics Data System (ADS)

Hughitt, V. K.; Ireland, J.; Mueller, D.

2011-12-01

Helioviewer.org is a free and open-source web application for exploring solar physics data in a simple and intuitive manner. Over the past several years, Helioviewer.org has enabled thousands of users from across the globe to explore the inner heliosphere, providing access to over ten million images from the SOHO, SDO, and STEREO missions. While Helioviewer.org has seen a surge in use by the public in recent months, it is still ultimately a science tool. The newest version of Helioviewer.org provides access to science-quality data for all available images through the Virtual Solar Observatory (VSO). In addition to providing a powerful platform for browsing heterogeneous sets of solar data, Helioviewer.org also seeks to be as flexible and extensible as possible, providing access to much of its functionality via a simple Application Programming Interface (API). Recently, the Helioviewer.org API was used for two such applications: a Wordpress plugin, and a Python library for solar physics data analysis (SunPy). These applications are discussed and examples of API usage are provided. Finally, Helioviewer.org is undergoing continual development, with new features being added on a regular basis. Recent updates to Helioviewer.org are discussed, along with a preview of things to come.

Kinetic Modeling of Accelerated Stability Testing Enabled by Second Harmonic Generation Microscopy.

PubMed

Song, Zhengtian; Sarkar, Sreya; Vogt, Andrew D; Danzer, Gerald D; Smith, Casey J; Gualtieri, Ellen J; Simpson, Garth J

2018-04-03

The low limits of detection afforded by second harmonic generation (SHG) microscopy coupled with image analysis algorithms enabled quantitative modeling of the temperature-dependent crystallization of active pharmaceutical ingredients (APIs) within amorphous solid dispersions (ASDs). ASDs, in which an API is maintained in an amorphous state within a polymer matrix, are finding increasing use to address solubility limitations of small-molecule APIs. Extensive stability testing is typically performed for ASD characterization, the time frame for which is often dictated by the earliest detectable onset of crystal formation. Here a study of accelerated stability testing on ritonavir, a human immunodeficiency virus (HIV) protease inhibitor, has been conducted. Under the condition for accelerated stability testing at 50 °C/75%RH and 40 °C/75%RH, ritonavir crystallization kinetics from amorphous solid dispersions were monitored by SHG microscopy. SHG microscopy coupled by image analysis yielded limits of detection for ritonavir crystals as low as 10 ppm, which is about 2 orders of magnitude lower than other methods currently available for crystallinity detection in ASDs. The four decade dynamic range of SHG microscopy enabled quantitative modeling with an established (JMAK) kinetic model. From the SHG images, nucleation and crystal growth rates were independently determined.

Extensive population admixture on drone congregation areas of the giant honeybee, Apis dorsata (Fabricius, 1793).

PubMed

Beaurepaire, Alexis L; Kraus, Bernard F; Koeniger, Gudrun; Koeniger, Nikolaus; Lim, Herbert; Moritz, Robin F A

2014-12-01

The giant honeybee Apis dorsata often forms dense colony aggregations which can include up to 200 often closely related nests in the same location, setting the stage for inbred matings. Yet, like in all other Apis species, A. dorsata queens mate in mid-air on lek like drone congregation areas (DCAs) where large numbers of males gather in flight. We here report how the drone composition of A. dorsata DCAs facilitates outbreeding, taking into the account both spatial (three DCAs) and temporal (subsequent sampling days) dynamics. We compared the drones' genotypes at ten microsatellite DNA markers with those of the queen genotypes of six drone-producing colonies located close to the DCAs (Tenom, Sabah, Malaysia). None of 430 sampled drones originated from any of these nearby colonies. Moreover, we estimated that 141 unidentified colonies were contributing to the three DCAs. Most of these colonies were participating multiple times in the different locations and/or during the consecutive days of sampling. The drones sampled in the DCAs could be attributed to six subpopulations. These were all admixed in all DCA samples, increasing the effective population size an order of magnitude and preventing matings between potentially related queens and drones.

Extensive population admixture on drone congregation areas of the giant honeybee, Apis dorsata (Fabricius, 1793)

PubMed Central

Beaurepaire, Alexis L; Kraus, Bernard F; Koeniger, Gudrun; Koeniger, Nikolaus; Lim, Herbert; Moritz, Robin F A

2014-01-01

The giant honeybee Apis dorsata often forms dense colony aggregations which can include up to 200 often closely related nests in the same location, setting the stage for inbred matings. Yet, like in all other Apis species, A. dorsata queens mate in mid-air on lek like drone congregation areas (DCAs) where large numbers of males gather in flight. We here report how the drone composition of A. dorsata DCAs facilitates outbreeding, taking into the account both spatial (three DCAs) and temporal (subsequent sampling days) dynamics. We compared the drones’ genotypes at ten microsatellite DNA markers with those of the queen genotypes of six drone-producing colonies located close to the DCAs (Tenom, Sabah, Malaysia). None of 430 sampled drones originated from any of these nearby colonies. Moreover, we estimated that 141 unidentified colonies were contributing to the three DCAs. Most of these colonies were participating multiple times in the different locations and/or during the consecutive days of sampling. The drones sampled in the DCAs could be attributed to six subpopulations. These were all admixed in all DCA samples, increasing the effective population size an order of magnitude and preventing matings between potentially related queens and drones. PMID:25558361

Shuttle-Data-Tape XML Translator

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

JSDTImport is a computer program for translating native Shuttle Data Tape (SDT) files from American Standard Code for Information Interchange (ASCII) format into databases in other formats. JSDTImport solves the problem of organizing the SDT content, affording flexibility to enable users to choose how to store the information in a database to better support client and server applications. JSDTImport can be dynamically configured by use of a simple Extensible Markup Language (XML) file. JSDTImport uses this XML file to define how each record and field will be parsed, its layout and definition, and how the resulting database will be structured. JSDTImport also includes a client application programming interface (API) layer that provides abstraction for the data-querying process. The API enables a user to specify the search criteria to apply in gathering all the data relevant to a query. The API can be used to organize the SDT content and translate into a native XML database. The XML format is structured into efficient sections, enabling excellent query performance by use of the XPath query language. Optionally, the content can be translated into a Structured Query Language (SQL) database for fast, reliable SQL queries on standard database server computers.

A SNP based high-density linkage map of Apis cerana reveals a high recombination rate similar to Apis mellifera.

PubMed

Shi, Yuan Yuan; Sun, Liang Xian; Huang, Zachary Y; Wu, Xiao Bo; Zhu, Yong Qiang; Zheng, Hua Jun; Zeng, Zhi Jiang

2013-01-01

The Eastern honey bee, Apis cerana Fabricius, is distributed in southern and eastern Asia, from India and China to Korea and Japan and southeast to the Moluccas. This species is also widely kept for honey production besides Apis mellifera. Apis cerana is also a model organism for studying social behavior, caste determination, mating biology, sexual selection, and host-parasite interactions. Few resources are available for molecular research in this species, and a linkage map was never constructed. A linkage map is a prerequisite for quantitative trait loci mapping and for analyzing genome structure. We used the Chinese honey bee, Apis cerana cerana to construct the first linkage map in the Eastern honey bee. F2 workers (N = 103) were genotyped for 126,990 single nucleotide polymorphisms (SNPs). After filtering low quality and those not passing the Mendel test, we obtained 3,000 SNPs, 1,535 of these were informative and used to construct a linkage map. The preliminary map contains 19 linkage groups, we then mapped the 19 linkage groups to 16 chromosomes by comparing the markers to the genome of A. mellfiera. The final map contains 16 linkage groups with a total of 1,535 markers. The total genetic distance is 3,942.7 centimorgans (cM) with the largest linkage group (180 loci) measuring 574.5 cM. Average marker interval for all markers across the 16 linkage groups is 2.6 cM. We constructed a high density linkage map for A. c. cerana with 1,535 markers. Because the map is based on SNP markers, it will enable easier and faster genotyping assays than randomly amplified polymorphic DNA or microsatellite based maps used in A. mellifera.

Globus: Service and Platform for Research Data Lifecycle Management

NASA Astrophysics Data System (ADS)

Ananthakrishnan, R.; Foster, I.

2017-12-01

Globus offers a range of data management capabilities to the community as hosted services, encompassing data transfer and sharing, user identity and authorization, and data publication. Globus capabilities are accessible via both a web browser and REST APIs. Web access allows researchers to use Globus capabilities through a software-as-a-service model; and the REST APIs address the needs of developers of research services, who can now use Globus as a platform, outsourcing complex user and data management tasks to Globus services. In this presentation, we review Globus capabilities and outline how it is being applied as a platform for scientific services, and highlight work done to link computational analysis flows to the underlying data through an interactive Jupyter notebook environment to promote immediate data usability, reusability of these flows by other researchers, and future analysis extensibility.

Quantitative analysis and comparative study of four cities green pattern in API system on the background of big data

NASA Astrophysics Data System (ADS)

Xin, YANG; Si-qi, WU; Qi, ZHANG

2018-05-01

Beijing, London, Paris, New York are typical cities in the world, so comparative study of four cities green pattern is very important to find out gap and advantage and to learn from each other. The paper will provide basis and new ideas for development of metropolises in China. On the background of big data, API (Application Programming Interface) system can provide extensive and accurate basic data to study urban green pattern in different geographical environment in domestic and foreign. On the basis of this, Average nearest neighbor tool, Kernel density tool and Standard Ellipse tool in ArcGIS platform can process and summarize data and realize quantitative analysis of green pattern. The paper summarized uniqueness of four cities green pattern and reasons of formation on basis of numerical comparison.

Polyoxylglycerides and glycerides: effects of manufacturing parameters on API stability, excipient functionality and processing.

PubMed

Jannin, Vincent; Rodier, Jean-David; Musakhanian, Jasmine

2014-05-15

Lipid-based formulations are a viable option to address modern drug delivery challenges such as increasing the oral bioavailability of poorly water-soluble active pharmaceutical ingredients (APIs), or sustaining the drug release of molecules intended for chronic diseases. Esters of fatty acids and glycerol (glycerides) and polyethylene-glycols (polyoxylglycerides) are two main classes of lipid-based excipients used by oral, dermal, rectal, vaginal or parenteral routes. These lipid-based materials are more and more commonly used in pharmaceutical drug products but there is still a lack of understanding of how the manufacturing processes, processing aids, or additives can impact the chemical stability of APIs within the drug product. In that regard, this review summarizes the key parameters to look at when formulating with lipid-based excipients in order to anticipate a possible impact on drug stability or variation of excipient functionality. The introduction presents the chemistry of natural lipids, fatty acids and their properties in relation to the extraction and refinement processes. Then, the key parameters during the manufacturing process influencing the quality of lipid-based excipients are provided. Finally, their critical characteristics are discussed in relation with their intended functionality and ability to interact with APIs and others excipients within the formulation. Copyright © 2014. Published by Elsevier B.V.

Use of an innovative T-tube maze assay and the proboscis extension response assay to assess sublethal effects of GM products and pesticides on learning capacity of the honey bee Apis mellifera L.

PubMed Central

Han, Peng; Lei, Chao-Liang; Cui, Jin-Jie; Desneux, Nicolas

2010-01-01

Transgenic Cry1Ac+CpTI cotton (CCRI41) is a promising cotton cultivar throughout China but side effects and especially sublethal effects of this transgenic cultivar on beneficial insects remain poorly studied. More specifically potential sublethal effects on behavioural traits of the honey bee Apis mellifera L. have not been formally assessed despite the importance of honey bees for pollination. The goal of our study was to assess potential effects of CCRI41 cotton pollen on visual and olfactory learning by honey bees. After a 7-day oral chronic exposure to honey mixed with either CCRI41 pollen, imidacloprid-treated conventional pollen (used as positive sublethal control) or conventional pollen (control), learning performance was evaluated by the classical proboscis extension reflex (PER) procedure as well as a T-tube maze test. The latter assay was designed as a new device to assess potential side effects of pesticides on visual associative learning of honey bees. These two procedures were complementary because the former focused on olfactory learning while the latter was involved in visual learning based on visual orientation ability. Oral exposure to CCRI41 pollen did not affect learning capacities of honey bees in both the T-tube maze and PER tests. However, exposure to imidacloprid resulted in reduced visual learning capacities in T-tube maze evaluation and decreased olfactory learning performances measured with PER. The implications of these results are discussed in terms of risks of transgenic CCRI41 cotton crops for honey bees. PMID:20872243

Development Roadmap of an Evolvable and Extensible Multi-Mission Telecom Planning and Analysis Framework

NASA Technical Reports Server (NTRS)

Cheung, Kar-Ming; Tung, Ramona H.; Lee, Charles H.

2003-01-01

In this paper, we describe the development roadmap and discuss the various challenges of an evolvable and extensible multi-mission telecom planning and analysis framework. Our long-term goal is to develop a set of powerful flexible telecommunications analysis tools that can be easily adapted to different missions while maintain the common Deep Space Communication requirements. The ability of re-using the DSN ground models and the common software utilities in our adaptations has contributed significantly to our development efforts measured in terms of consistency, accuracy, and minimal effort redundancy, which can translate into shorter development time and major cost savings for the individual missions. In our roadmap, we will address the design principles, technical achievements and the associated challenges for following telecom analysis tools (i) Telecom Forecaster Predictor - TFP (ii) Unified Telecom Predictor - UTP (iii) Generalized Telecom Predictor - GTP (iv) Generic TFP (v) Web-based TFP (vi) Application Program Interface - API (vii) Mars Relay Network Planning Tool - MRNPT.

Enabling Mobile Air Quality App Development with an AirNow API

NASA Astrophysics Data System (ADS)

Dye, T.; White, J. E.; Ludewig, S. A.; Dickerson, P.; Healy, A. N.; West, J. W.; Prince, L. A.

2013-12-01

The U.S. Environmental Protection Agency's (EPA) AirNow program works with over 130 participating state, local, and federal air quality agencies to obtain, quality control, and store real-time air quality observations and forecasts. From these data, the AirNow system generates thousands of maps and products each hour. Each day, information from AirNow is published online and in other media to assist the public in making health-based decisions related to air quality. However, an increasing number of people use mobile devices as their primary tool for obtaining information, and AirNow has responded to this trend by publishing an easy-to-use Web API that is useful for mobile app developers. This presentation will describe the various features of the AirNow application programming interface (API), including Representational State Transfer (REST)-type web services, file outputs, and RSS feeds. In addition, a web portal for the AirNow API will be shown, including documentation on use of the system, a query tool for configuring and running web services, and general information about the air quality data and forecasts available. Data published via the AirNow API includes corresponding Air Quality Index (AQI) levels for each pollutant. We will highlight examples of mobile apps that are using the AirNow API to provide location-based, real-time air quality information. Examples will include mobile apps developed for Minnesota ('Minnesota Air') and Washington, D.C. ('Clean Air Partners Air Quality'), and an app developed by EPA ('EPA AirNow').

Apis - a Digital Inventory of Archaeological Heritage Based on Remote Sensing Data

NASA Astrophysics Data System (ADS)

Doneus, M.; Forwagner, U.; Liem, J.; Sevara, C.

2017-08-01

Heritage managers are in need of dynamic spatial inventories of archaeological and cultural heritage that provide them with multipurpose tools to interactively understand information about archaeological heritage within its landscape context. Specifically, linking site information with the respective non-invasive prospection data is of increasing importance as it allows for the assessment of inherent uncertainties related to the use and interpretation of remote sensing data by the educated and knowledgeable heritage manager. APIS, the archaeological prospection information system of the Aerial Archive of the University of Vienna, is specifically designed to meet these needs. It provides storage and easy access to all data concerning aerial photographs and archaeological sites through a single GIS-based application. Furthermore, APIS has been developed in an open source environment, which allows it to be freely distributed and modified. This combination in one single open source system facilitates an easy workflow for data management, interpretation, storage, and retrieval. APIS and a sample dataset will be released free of charge under creative commons license in near future.

Home Energy Scoring Tools (website) and Application Programming Interfaces, APIs (aka HEScore)

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

Mills, Evan; Bourassa, Norm; Rainer, Leo

A web-based residential energy rating tool with APIs that runs the LBNL website: Provides customized estimates of residential energy use and energy bills based on building description information provided by the user. Energy use is estimated using engineering models developed at LBNL. Space heating and cooling use is based on the DOE-2. 1E building simulation model. Other end-users (water heating, appliances, lighting, and misc. equipment) are based on engineering models developed by LBNL.

Home Energy Scoring Tools (website) and Application Programming Interfaces, APIs (aka HEScore)

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

Mills, Evan; Bourassa, Norm; Rainer, Leo

2016-04-22

A web-based residential energy rating tool with APIs that runs the LBNL website: Provides customized estimates of residential energy use and energy bills based on building description information provided by the user. Energy use is estimated using engineering models developed at LBNL. Space heating and cooling use is based on the DOE-2. 1E building simulation model. Other end-users (water heating, appliances, lighting, and misc. equipment) are based on engineering models developed by LBNL.

The temporal and spatial distribution characteristics of air pollution index and meteorological elements in Beijing, Tianjin and Shijiazhuang, China.

PubMed

Huading, Shi; Critto, Andrea; Torresan, Silvia; Qingxian, Gao

2018-06-13

With the rapid economic development and the continuous population growth, several important cities in China suffer serious air pollution, especially in the Beijing-Tianjin-Hebei economic developing area. Based on the daily air pollution index (API) and surface meteorological elements in Beijing, Tianjin and Shijiazhuang from 2001 to 2010, the relationships between API and meteorological elements were analyzed. The statistical analysis focused on the relationships at seasonal and monthly average scales, on different air pollution grades and air pollution processes. The results revealed that the air pollution conditions in the three areas gradually improved from 2001 to 2010, especially during summer; and the worst conditions in air quality were recorded in Beijing in spring due to the influences of dust, while in Tianjin and Shijiazhuang in winter due to household heating. Meteorological elements exhibited different influences on air pollution, showing similar relationships between API in monthly averages and four meteorological elements (i.e., the average, maximum and minimum temperatures, maximum air pressure, vapor pressure, and maximum wind speed); while the relationships on a seasonal average scale demonstrated significant differences. Compared with seasonal and monthly average scales of API, the relation coefficients based on different air pollution grades were significatively lower; while the relationship between API and meteorological elements based on air pollution process reduced the smoothing effect due to the average processing of seasonal and monthly API and improved the accuracy of the results based on different air pollution grades. Finally, statistical analysis of the distribution of pollution days in different wind directions indicated the directions of extreme and maximum wind speeds that mainly influence air pollution; representing a valuable information that could support the definition of air pollution control strategies through the identification of the regions (and the located emission sources) where to focus the implementation of emission reduction actions. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

A RESTful API for accessing microbial community data for MG-RAST.

PubMed

Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M; Desai, Narayan; Meyer, Folker

2015-01-01

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http://kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase's microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.

Populus euphratica APYRASE2 Enhances Cold Tolerance by Modulating Vesicular Trafficking and Extracellular ATP in Arabidopsis Plants.

PubMed

Deng, Shurong; Sun, Jian; Zhao, Rui; Ding, Mingquan; Zhang, Yinan; Sun, Yuanling; Wang, Wei; Tan, Yeqing; Liu, Dandan; Ma, Xujun; Hou, Peichen; Wang, Meijuan; Lu, Cunfu; Shen, Xin; Chen, Shaoliang

2015-09-01

Apyrase and extracellular ATP play crucial roles in mediating plant growth and defense responses. In the cold-tolerant poplar, Populus euphratica, low temperatures up-regulate APYRASE2 (PeAPY2) expression in callus cells. We investigated the biochemical characteristics of PeAPY2 and its role in cold tolerance. We found that PeAPY2 predominantly localized to the plasma membrane, but punctate signals also appeared in the endoplasmic reticulum and Golgi apparatus. PeAPY2 exhibited broad substrate specificity, but it most efficiently hydrolyzed purine nucleotides, particularly ATP. PeAPY2 preferred Mg(2+) as a cofactor, and it was insensitive to various, specific ATPase inhibitors. When PeAPY2 was ectopically expressed in Arabidopsis (Arabidopsis thaliana), cold tolerance was enhanced, based on root growth measurements and survival rates. Moreover, under cold stress, PeAPY2-transgenic plants maintained plasma membrane integrity and showed reduced cold-elicited electrolyte leakage compared with wild-type plants. These responses probably resulted from efficient plasma membrane repair via vesicular trafficking. Indeed, transgenic plants showed accelerated endocytosis and exocytosis during cold stress and recovery. We found that low doses of extracellular ATP accelerated vesicular trafficking, but high extracellular ATP inhibited trafficking and reduced cell viability. Cold stress caused significant increases in root medium extracellular ATP. However, under these conditions, PeAPY2-transgenic lines showed greater control of extracellular ATP levels than wild-type plants. We conclude that Arabidopsis plants that overexpressed PeAPY2 could increase membrane repair by accelerating vesicular trafficking and hydrolyzing extracellular ATP to avoid excessive, cold-elicited ATP accumulation in the root medium and, thus, reduced ATP-induced inhibition of vesicular trafficking. © 2015 American Society of Plant Biologists. All Rights Reserved.

Navigation API Route Fuel Saving Opportunity Assessment on Large-Scale Real-World Travel Data for Conventional Vehicles and Hybrid Electric Vehicles: Preprint

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

Zhu, Lei; Holden, Jacob; Gonder, Jeffrey D

The green routing strategy instructing a vehicle to select a fuel-efficient route benefits the current transportation system with fuel-saving opportunities. This paper introduces a navigation API route fuel-saving evaluation framework for estimating fuel advantages of alternative API routes based on large-scale, real-world travel data for conventional vehicles (CVs) and hybrid electric vehicles (HEVs). The navigation APIs, such Google Directions API, integrate traffic conditions and provide feasible alternative routes for origin-destination pairs. This paper develops two link-based fuel-consumption models stratified by link-level speed, road grade, and functional class (local/non-local), one for CVs and the other for HEVs. The link-based fuel-consumption modelsmore » are built by assigning travel from a large number of GPS driving traces to the links in TomTom MultiNet as the underlying road network layer and road grade data from a U.S. Geological Survey elevation data set. Fuel consumption on a link is calculated by the proposed fuel consumption model. This paper envisions two kinds of applications: 1) identifying alternate routes that save fuel, and 2) quantifying the potential fuel savings for large amounts of travel. An experiment based on a large-scale California Household Travel Survey GPS trajectory data set is conducted. The fuel consumption and savings of CVs and HEVs are investigated. At the same time, the trade-off between fuel saving and time saving for choosing different routes is also examined for both powertrains.« less

The Role of Vision and Mechanosensation in Insect Flight Control

DTIC Science & Technology

2012-01-01

intensity. We used bumblebees (Bombus terrestris), honeybees ( Apis mellifera ), the common wasp (Vespa vulgaris), hornets (Vespa crabro) flies (Mousca...bees ( Apis mellifera L.). J. Exp. Biol. 209, 978-984. Beyeler, A., Zufferey, J.-C. and Floreano, D. (2009). Vision-based control of near- obstacle

Taxonomic relevance of an adverse outcome pathway network considering apis and non-apis bees

EPA Science Inventory

Product Description: The US EPA is developing more cost effective and efficient ways to evaluate chemical safety using high throughput and computationally based testing strategies. An important component of this approach is the ability to translate chemical effects on fundamental...

Automated chart review utilizing natural language processing algorithm for asthma predictive index.

PubMed

Kaur, Harsheen; Sohn, Sunghwan; Wi, Chung-Il; Ryu, Euijung; Park, Miguel A; Bachman, Kay; Kita, Hirohito; Croghan, Ivana; Castro-Rodriguez, Jose A; Voge, Gretchen A; Liu, Hongfang; Juhn, Young J

2018-02-13

Thus far, no algorithms have been developed to automatically extract patients who meet Asthma Predictive Index (API) criteria from the Electronic health records (EHR) yet. Our objective is to develop and validate a natural language processing (NLP) algorithm to identify patients that meet API criteria. This is a cross-sectional study nested in a birth cohort study in Olmsted County, MN. Asthma status ascertained by manual chart review based on API criteria served as gold standard. NLP-API was developed on a training cohort (n = 87) and validated on a test cohort (n = 427). Criterion validity was measured by sensitivity, specificity, positive predictive value and negative predictive value of the NLP algorithm against manual chart review for asthma status. Construct validity was determined by associations of asthma status defined by NLP-API with known risk factors for asthma. Among the eligible 427 subjects of the test cohort, 48% were males and 74% were White. Median age was 5.3 years (interquartile range 3.6-6.8). 35 (8%) had a history of asthma by NLP-API vs. 36 (8%) by abstractor with 31 by both approaches. NLP-API predicted asthma status with sensitivity 86%, specificity 98%, positive predictive value 88%, negative predictive value 98%. Asthma status by both NLP and manual chart review were significantly associated with the known asthma risk factors, such as history of allergic rhinitis, eczema, family history of asthma, and maternal history of smoking during pregnancy (p value < 0.05). Maternal smoking [odds ratio: 4.4, 95% confidence interval 1.8-10.7] was associated with asthma status determined by NLP-API and abstractor, and the effect sizes were similar between the reviews with 4.4 vs 4.2 respectively. NLP-API was able to ascertain asthma status in children mining from EHR and has a potential to enhance asthma care and research through population management and large-scale studies when identifying children who meet API criteria.

Genetic diversity of the Dwarf honeybee (Apis florea Fabricius, 1787) populations based on microsatellite markers.

PubMed

Asadi, N; Rahimi, A; Ghaheri, M; Kahrizi, D; Bagheri Dehbaghi, M; Khederzadeh, S; Banabazi, M H; Esmaeilkhanian, S; Veisi, B; Geravandi, M; Karim, H; Vaziri, S; Daneshgar, F; Zargooshi, J

2016-10-31

Apis florea is one of two species of small, wild honeybee. The present study was conducted to evaluate the genetic diversity of Apis florea honeybee from 48 nests (colonies) using microsatellite markers in the South of Iran. All honeybee samples were analyzed for six microsatellite loci (A88, A107, A7, B124, A113 and A35). The six loci had different numbers of alleles in the sampled colonies ranging from 7 (loci A107) to 3 (loci A7, A35). Gene diversity in Apis florea ranged from 0.491 to 0.595. This range probably reflects the spreading of nests in a large region with a varied climate. Phylogenetic tree showed two distinct clusters including a) Minab region samples and b) Bandar Abbas, Bandar Khamir and Qeshm Island regions. All of these regions are geographically rich, having varied vegetation and climate conditions. Our findings are an important contribution to the methods of studying distribution and conservation of Apis florea.

Distributed nuclear medicine applications using World Wide Web and Java technology.

PubMed

Knoll, P; Höll, K; Mirzaei, S; Koriska, K; Köhn, H

2000-01-01

At present, medical applications applying World Wide Web (WWW) technology are mainly used to view static images and to retrieve some information. The Java platform is a relative new way of computing, especially designed for network computing and distributed applications which enables interactive connection between user and information via the WWW. The Java 2 Software Development Kit (SDK) including Java2D API, Java Remote Method Invocation (RMI) technology, Object Serialization and the Java Advanced Imaging (JAI) extension was used to achieve a robust, platform independent and network centric solution. Medical image processing software based on this technology is presented and adequate performance capability of Java is demonstrated by an iterative reconstruction algorithm for single photon emission computerized tomography (SPECT).

Performance indicators for carrier-based DPIs: Carrier surface properties for capsule filling and API properties for in vitro aerosolisation.

PubMed

Faulhammer, E; Zellnitz, S; Wutscher, T; Stranzinger, S; Zimmer, A; Paudel, A

2018-01-30

This study investigates engineered carrier, as well as engineered API particles, and shows that there are distinct performance indicators of particle engineering for carrier-based dry powder inhalers (DPIs). Spray dried (SDSS) and jet-milled (JMSS) salbutamol sulphate (SS) was blended with untreated α-lactose monohydrate (LAC_R) and α-lactose monohydrate engineered (LAC_E). Subsequent capsule filling was performed with different process settings on a dosator nozzle capsule filling machine in order to reach a target fill weight of 20-25 mg. To evaluate the performance of the different mixtures, in vitro lung deposition experiments were carried out with a next generation impactor, the emitted dose (ED) and fine particle fraction (FPF) were calculated based on the specification of the European pharmacopoeia. The FPF of micronised powder blends is significantly higher (20%) compared to the FPF of spray dried blends (5%). Compared to API engineering, carrier engineering had a positive effect on the capsule filling performance (weight variability and mean fill weight) at lower compression ratios (setting 1). Results further showed that higher compression ratios appear to be beneficial in terms of capsule filling performance (higher fill weight and less fill weight variation). Concluding, it can be stated that the carrier engineering, or generally carrier properties, govern downstream processing, whereas the API engineering and API properties govern the aerosolisation performance and thereby significantly affect the dose delivery to the lungs. Copyright © 2017 Elsevier B.V. All rights reserved.

Integration of Experience API Into CDET’s E-Learning

DTIC Science & Technology

2016-06-01

based on customers ’ actual usage on a transaction basis. Value-based Penetration Pricing • Market segments where buyers have high price...they need to accomplish the course learning objectives (see Figure 6). This method allows each student to customize their own learning experiences ... EXPERIENCE API INTO CDET’S E- LEARNING by Clayton C. MacAloney June 2016 Thesis Advisor: Man-Tak Shing Co-Advisor: Arijit Das THIS PAGE

Reactome Pengine: A web-logic API to the homo sapiens reactome.

PubMed

Neaves, Samuel R; Tsoka, Sophia; Millard, Louise A C

2018-03-30

Existing ways of accessing data from the Reactome database are limited. Either a researcher is restricted to particular queries defined by a web application programming interface (API), or they have to download the whole database. Reactome Pengine is a web service providing a logic programming based API to the human reactome. This gives researchers greater flexibility in data access than existing APIs, as users can send their own small programs (alongside queries) to Reactome Pengine. The server and an example notebook can be found at https://apps.nms.kcl.ac.uk/reactome-pengine. Source code is available at https://github.com/samwalrus/reactome-pengine and a Docker image is available at https://hub.docker.com/r/samneaves/rp4/ . samuel.neaves@kcl.ac.uk. Supplementary data are available at Bioinformatics online.

Effects of C and Si on strain aging of strain-based API X60 pipeline steels

NASA Astrophysics Data System (ADS)

Sung, Hyo Kyung; Lee, Dong Ho; Lee, Sunghak; Lee, Byeong-Joo; Hong, Seung-Pyo; Kim, Young-Woon; Yoo, Jang Yong; Hwang, Byoungchul; Shin, Sang Yong

2017-05-01

Four types of strain-based API X60 pipeline steels were fabricated by varying the C and Si contents, and the effects of C and Si on strain aging were investigated. The 0.05 wt% C steels consisted mainly of polygonal ferrite (PF), whereas the 0.08 wt% C steels consisted of acicular ferrite (AF). The volume fraction of AF increased with increasing C content because C is an austenite stabilizer element. The volume fractions of bainitic ferrite (BF) of the 0.15 wt% Si steels were higher than those of the 0.25 wt% Si steels, whereas the volume fractions of the secondary phases were lower. From the tensile properties before and after the aging process of the strainbased API X60 pipeline steels, the yield strength increased and the uniform and total elongation decreased, which is the strain aging effect. The strain aging effect in the strain-based API X60 pipeline steels was minimized when the volume fraction of AF was increased and secondary phases were distributed uniformly. On the other hand, an excessively high C content formed fine precipitates, and the strain aging effect occurred because of the interactions among dislocations and fine precipitates.

uPy: a ubiquitous CG Python API with biological-modeling applications.

PubMed

Autin, Ludovic; Johnson, Graham; Hake, Johan; Olson, Arthur; Sanner, Michel

2012-01-01

The uPy Python extension module provides a uniform abstraction of the APIs of several 3D computer graphics programs (called hosts), including Blender, Maya, Cinema 4D, and DejaVu. A plug-in written with uPy can run in all uPy-supported hosts. Using uPy, researchers have created complex plug-ins for molecular and cellular modeling and visualization. uPy can simplify programming for many types of projects (not solely science applications) intended for multihost distribution. It's available at http://upy.scripps.edu. The first featured Web extra is a video that shows interactive analysis of a calcium dynamics simulation. YouTube URL: http://youtu.be/wvs-nWE6ypo. The second featured Web extra is a video that shows rotation of the HIV virus. YouTube URL: http://youtu.be/vEOybMaRoKc.

Cyclic Nucleotide-Gated Channels, Calmodulin, Adenylyl Cyclase, and Calcium/Calmodulin-Dependent Protein Kinase II Are Required for Late, but Not Early, Long-Term Memory Formation in the Honeybee

ERIC Educational Resources Information Center

Matsumoto, Yukihisa; Sandoz, Jean-Christophe; Devaud, Jean-Marc; Lormant, Flore; Mizunami, Makoto; Giurfa, Martin

2014-01-01

Memory is a dynamic process that allows encoding, storage, and retrieval of information acquired through individual experience. In the honeybee "Apis mellifera," olfactory conditioning of the proboscis extension response (PER) has shown that besides short-term memory (STM) and mid-term memory (MTM), two phases of long-term memory (LTM)…

Framework for Development and Distribution of Hardware Acceleration

NASA Astrophysics Data System (ADS)

Thomas, David B.; Luk, Wayne W.

2002-07-01

This paper describes IGOL, a framework for developing reconfigurable data processing applications. While IGOL was originally designed to target imaging and graphics systems, its structure is sufficiently general to support a broad range of applications. IGOL adopts a four-layer architecture: application layer, operation layer, appliance layer and configuration layer. This architecture is intended to separate and co-ordinate both the development and execution of hardware and software components. Hardware developers can use IGOL as an instance testbed for verification and benchmarking, as well as for distribution. Software application developers can use IGOL to discover hardware accelerated data processors, and to access them in a transparent, non-hardware specific manner. IGOL provides extensive support for the RC1000-PP board via the Handel-C language, and a wide selection of image processing filters have been developed. IGOL also supplies plug-ins to enable such filters to be incorporated in popular applications such as Premiere, Winamp, VirtualDub and DirectShow. Moreover, IGOL allows the automatic use of multiple cards to accelerate an application, demonstrated using DirectShow. To enable transparent acceleration without sacrificing performance, a three-tiered COM (Component Object Model) API has been designed and implemented. This API provides a well-defined and extensible interface which facilitates the development of hardware data processors that can accelerate multiple applications.

Enabling Cross-Platform Clinical Decision Support through Web-Based Decision Support in Commercial Electronic Health Record Systems: Proposal and Evaluation of Initial Prototype Implementations

PubMed Central

Zhang, Mingyuan; Velasco, Ferdinand T.; Musser, R. Clayton; Kawamoto, Kensaku

2013-01-01

Enabling clinical decision support (CDS) across multiple electronic health record (EHR) systems has been a desired but largely unattained aim of clinical informatics, especially in commercial EHR systems. A potential opportunity for enabling such scalable CDS is to leverage vendor-supported, Web-based CDS development platforms along with vendor-supported application programming interfaces (APIs). Here, we propose a potential staged approach for enabling such scalable CDS, starting with the use of custom EHR APIs and moving towards standardized EHR APIs to facilitate interoperability. We analyzed three commercial EHR systems for their capabilities to support the proposed approach, and we implemented prototypes in all three systems. Based on these analyses and prototype implementations, we conclude that the approach proposed is feasible, already supported by several major commercial EHR vendors, and potentially capable of enabling cross-platform CDS at scale. PMID:24551426

From WSN towards WoT: Open API Scheme Based on oneM2M Platforms.

PubMed

Kim, Jaeho; Choi, Sung-Chan; Ahn, Il-Yeup; Sung, Nak-Myoung; Yun, Jaeseok

2016-10-06

Conventional computing systems have been able to be integrated into daily objects and connected to each other due to advances in computing and network technologies, such as wireless sensor networks (WSNs), forming a global network infrastructure, called the Internet of Things (IoT). To support the interconnection and interoperability between heterogeneous IoT systems, the availability of standardized, open application programming interfaces (APIs) is one of the key features of common software platforms for IoT devices, gateways, and servers. In this paper, we present a standardized way of extending previously-existing WSNs towards IoT systems, building the world of the Web of Things (WoT). Based on the oneM2M software platforms developed in the previous project, we introduce a well-designed open API scheme and device-specific thing adaptation software (TAS) enabling WSN elements, such as a wireless sensor node, to be accessed in a standardized way on a global scale. Three pilot services are implemented (i.e., a WiFi-enabled smart flowerpot, voice-based control for ZigBee-connected home appliances, and WiFi-connected AR.Drone control) to demonstrate the practical usability of the open API scheme and TAS modules. Full details on the method of integrating WSN elements into three example systems are described at the programming code level, which is expected to help future researchers in integrating their WSN systems in IoT platforms, such as oneM2M. We hope that the flexibly-deployable, easily-reusable common open API scheme and TAS-based integration method working with the oneM2M platforms will help the conventional WSNs in diverse industries evolve into the emerging WoT solutions.

From WSN towards WoT: Open API Scheme Based on oneM2M Platforms

PubMed Central

Kim, Jaeho; Choi, Sung-Chan; Ahn, Il-Yeup; Sung, Nak-Myoung; Yun, Jaeseok

2016-01-01

Conventional computing systems have been able to be integrated into daily objects and connected to each other due to advances in computing and network technologies, such as wireless sensor networks (WSNs), forming a global network infrastructure, called the Internet of Things (IoT). To support the interconnection and interoperability between heterogeneous IoT systems, the availability of standardized, open application programming interfaces (APIs) is one of the key features of common software platforms for IoT devices, gateways, and servers. In this paper, we present a standardized way of extending previously-existing WSNs towards IoT systems, building the world of the Web of Things (WoT). Based on the oneM2M software platforms developed in the previous project, we introduce a well-designed open API scheme and device-specific thing adaptation software (TAS) enabling WSN elements, such as a wireless sensor node, to be accessed in a standardized way on a global scale. Three pilot services are implemented (i.e., a WiFi-enabled smart flowerpot, voice-based control for ZigBee-connected home appliances, and WiFi-connected AR.Drone control) to demonstrate the practical usability of the open API scheme and TAS modules. Full details on the method of integrating WSN elements into three example systems are described at the programming code level, which is expected to help future researchers in integrating their WSN systems in IoT platforms, such as oneM2M. We hope that the flexibly-deployable, easily-reusable common open API scheme and TAS-based integration method working with the oneM2M platforms will help the conventional WSNs in diverse industries evolve into the emerging WoT solutions. PMID:27782058

TH-D-BRB-04: Pinnacle Scripting: Improving Efficiency While Maintaining Safety

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

Moore, J.

2016-06-15

Scripting capabilities and application programming interfaces (APIs) are becoming commonly available in modern treatment planning systems. These links to the treatment planning system (TPS) allow users to read data from the TPS, and in some cases use TPS functionality and write data back to the TPS. Such tools are powerful extensions, allowing automation of routine clinical tasks and supporting research, particularly research involving repetitive tasks on large patient populations. The data and functionality exposed by scripting/API capabilities is vendor dependent, as are the languages used by script/API engines, such as the Microsoft .NET framework or Python. Scripts deployed in amore » clinical environment must be commissioned and validated like any other software tool. This session will provide an overview of scripting applications and a discussion of best practices, followed by a practical introduction to the scripting capabilities of three commercial treatment planning systems. Learning Objectives: Understand the scripting capabilities available in several treatment planning systems Learn how to get started using scripting capabilities Understand the best practices for safe script deployment in a clinical environment R. Popple, Varian Medical Systems has provided research support unrelated to the topic of this session.R. Cardan, Varian Medical Systems for grant research, product evaluation, and teaching honorarium.« less

Honey bee (Apis mellifera) nurses do not consume pollens based on their nutritional quality

USDA-ARS?s Scientific Manuscript database

Honey bees (Apis mellifera) consume a variety of pollens to meet the majority of their requirements for protein and lipids. Recent work indicates that at both the colony and individual levels, honey bees prefer diets that reflect the proper ratio of nutrients necessary for optimal survival and homeo...

Academic Peer Instruction: Reference and Training Manual (with Answers)

ERIC Educational Resources Information Center

Zaritsky, Joyce; Toce, Andi

2013-01-01

This manual consists of an introduction to our Academic Peer Instruction (API) program at LaGuardia Community College, a compilation of the materials we have developed and use for training of our tutors (with answers), and a bibliography. API is based on an internationally recognized peer tutoring program, Supplemental Instruction. (Contains 6…

Develop 3G Application with The J2ME SATSA API

NASA Astrophysics Data System (ADS)

JunWu, Xu; JunLing, Liang

This paper describes research in the use of the Security and Trust Services API for J2ME (SATSA) to develop mobile applications. for 3G networks. SATSA defines a set of APIs that allows J2ME applications to communicate with and access functionality, secure storage and cryptographic operations provided by security elements such as smart cards and Wireless Identification Modules (WIM). A Java Card application could also work as an authentication module in a J2ME-based e-bank application. The e-bank application would allow its users to access their bank accounts using their cell phones.

Design and Implement AN Interoperable Internet of Things Application Based on AN Extended Ogc Sensorthings Api Standard

NASA Astrophysics Data System (ADS)

Huang, C. Y.; Wu, C. H.

2016-06-01

The Internet of Things (IoT) is an infrastructure that interconnects uniquely-identifiable devices using the Internet. By interconnecting everyday appliances, various monitoring and physical mashup applications can be constructed to improve people's daily life. However, IoT devices created by different manufacturers follow different proprietary protocols and cannot communicate with each other. This heterogeneity issue causes different products to be locked in multiple closed ecosystems that we call IoT silos. In order to address this issue, a common industrial solution is the hub approach, which implements connectors to communicate with IoT devices following different protocols. However, with the growing number of proprietary protocols proposed by device manufacturers, IoT hubs need to support and maintain a lot of customized connectors. Hence, we believe the ultimate solution to address the heterogeneity issue is to follow open and interoperable standard. Among the existing IoT standards, the Open Geospatial Consortium (OGC) SensorThings API standard supports comprehensive conceptual model and query functionalities. The first version of SensorThings API mainly focuses on connecting to IoT devices and sharing sensor observations online, which is the sensing capability. Besides the sensing capability, IoT devices could also be controlled via the Internet, which is the tasking capability. While the tasking capability was not included in the first version of the SensorThings API standard, this research aims on defining the tasking capability profile and integrates with the SensorThings API standard, which we call the extended-SensorThings API in this paper. In general, this research proposes a lightweight JSON-based web service description, the "Tasking Capability Description", allowing device owners and manufacturers to describe different IoT device protocols. Through the extended- SensorThings API, users and applications can follow a coherent protocol to control IoT devices that use different communication protocols, which could consequently achieve the interoperable Internet of Things infrastructure.

Air pollution and case fatality of SARS in the People's Republic of China: an ecologic study

PubMed Central

Cui, Yan; Zhang, Zuo-Feng; Froines, John; Zhao, Jinkou; Wang, Hua; Yu, Shun-Zhang; Detels, Roger

2003-01-01

Background Severe acute respiratory syndrome (SARS) has claimed 349 lives with 5,327 probable cases reported in mainland China since November 2002. SARS case fatality has varied across geographical areas, which might be partially explained by air pollution level. Methods Publicly accessible data on SARS morbidity and mortality were utilized in the data analysis. Air pollution was evaluated by air pollution index (API) derived from the concentrations of particulate matter, sulfur dioxide, nitrogen dioxide, carbon monoxide and ground-level ozone. Ecologic analysis was conducted to explore the association and correlation between air pollution and SARS case fatality via model fitting. Partially ecologic studies were performed to assess the effects of long-term and short-term exposures on the risk of dying from SARS. Results Ecologic analysis conducted among 5 regions with 100 or more SARS cases showed that case fatality rate increased with the increment of API (case fatality = - 0.063 + 0.001 * API). Partially ecologic study based on short-term exposure demonstrated that SARS patients from regions with moderate APIs had an 84% increased risk of dying from SARS compared to those from regions with low APIs (RR = 1.84, 95% CI: 1.41–2.40). Similarly, SARS patients from regions with high APIs were twice as likely to die from SARS compared to those from regions with low APIs. (RR = 2.18, 95% CI: 1.31–3.65). Partially ecologic analysis based on long-term exposure to ambient air pollution showed the similar association. Conclusion Our studies demonstrated a positive association between air pollution and SARS case fatality in Chinese population by utilizing publicly accessible data on SARS statistics and air pollution indices. Although ecologic fallacy and uncontrolled confounding effect might have biased the results, the possibility of a detrimental effect of air pollution on the prognosis of SARS patients deserves further investigation. PMID:14629774

Integrated platform and API for electrophysiological data

PubMed Central

Sobolev, Andrey; Stoewer, Adrian; Leonhardt, Aljoscha; Rautenberg, Philipp L.; Kellner, Christian J.; Garbers, Christian; Wachtler, Thomas

2014-01-01

Recent advancements in technology and methodology have led to growing amounts of increasingly complex neuroscience data recorded from various species, modalities, and levels of study. The rapid data growth has made efficient data access and flexible, machine-readable data annotation a crucial requisite for neuroscientists. Clear and consistent annotation and organization of data is not only an important ingredient for reproducibility of results and re-use of data, but also essential for collaborative research and data sharing. In particular, efficient data management and interoperability requires a unified approach that integrates data and metadata and provides a common way of accessing this information. In this paper we describe GNData, a data management platform for neurophysiological data. GNData provides a storage system based on a data representation that is suitable to organize data and metadata from any electrophysiological experiment, with a functionality exposed via a common application programming interface (API). Data representation and API structure are compatible with existing approaches for data and metadata representation in neurophysiology. The API implementation is based on the Representational State Transfer (REST) pattern, which enables data access integration in software applications and facilitates the development of tools that communicate with the service. Client libraries that interact with the API provide direct data access from computing environments like Matlab or Python, enabling integration of data management into the scientist's experimental or analysis routines. PMID:24795616

Home Energy Management System - VOLTTRON Integration

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

Zandi, Helia

In most Home Energy Management Systems (HEMS) available in the market, different devices running different communication protocols cannot interact with each other and exchange information. As a result of this integration, the information about different devices running different communication protocol can be accessible by other agents and devices running on VOLTTRON platform. The integration process can be used by any HEMS available in the market regardless of the programming language they use. If the existing HEMS provides an Application Programming Interface (API) based on the RESTFul architecture, that API can be used for integration. Our candidate HEMS in this projectmore » is home-assistant (Hass). An agent is implemented which can communicate with the Hass API and receives information about the devices loaded on the API. The agent publishes the information it receives on the VOLTTRON message bus so other agents can have access to this information. On the other side, for each type of devices, an agent is implemented such as Climate Agent, Lock Agent, Switch Agent, Light Agent, etc. Each of these agents is subscribed to the messages published on the message bus about their associated devices. These agents can also change the status of the devices by sending appropriate service calls to the API. Other agents and services on the platform can also access this information and coordinate their decision-making process based on this information.« less

Integrated platform and API for electrophysiological data.

PubMed

Sobolev, Andrey; Stoewer, Adrian; Leonhardt, Aljoscha; Rautenberg, Philipp L; Kellner, Christian J; Garbers, Christian; Wachtler, Thomas

2014-01-01

Recent advancements in technology and methodology have led to growing amounts of increasingly complex neuroscience data recorded from various species, modalities, and levels of study. The rapid data growth has made efficient data access and flexible, machine-readable data annotation a crucial requisite for neuroscientists. Clear and consistent annotation and organization of data is not only an important ingredient for reproducibility of results and re-use of data, but also essential for collaborative research and data sharing. In particular, efficient data management and interoperability requires a unified approach that integrates data and metadata and provides a common way of accessing this information. In this paper we describe GNData, a data management platform for neurophysiological data. GNData provides a storage system based on a data representation that is suitable to organize data and metadata from any electrophysiological experiment, with a functionality exposed via a common application programming interface (API). Data representation and API structure are compatible with existing approaches for data and metadata representation in neurophysiology. The API implementation is based on the Representational State Transfer (REST) pattern, which enables data access integration in software applications and facilitates the development of tools that communicate with the service. Client libraries that interact with the API provide direct data access from computing environments like Matlab or Python, enabling integration of data management into the scientist's experimental or analysis routines.

The effects of honey (Apis dorsata) supplements on increased bone strength in ovariectomized rat as animal model of osteoporosis

NASA Astrophysics Data System (ADS)

Yudaniayanti, Ira Sari; Primarizky, Hardany; Nangoi, Lianny

2018-04-01

Osteoporosis is a chronic skeletal disease characterized by low bone mass and microarchitectural deterioration with a consequent increase in bone fragility and fracture risk. The aim of the study was to evaluate the effects of honey (Apis dorsata) supplements on increased bone strength in ovariectomized rat as animal models of osteoporosis. Twenty female rats at 3 months of age, weighing 150-200 g were used in the study. The rats were divided into five groups (n=4) : Sham operation group (SH); ovariectomy group no treatment(OVX); ovariectomy with treatment Apis dorsata 1g/Kg BW (AD-1); ovariectomy with treatment Apis dorsata 2g/Kg BW (AD-2); ovariectomy with treatment Apis dorsata 4g/Kg BW (AD-3). The treatment started to be given the next day after ovariectomy operation for 12 weeks. The Rats were sacrified within 12 weeks, and then the right femur were taken bone strength test. Based on the statistical analysis of the bone strength test, the greatest score belongs to the Sham operation group (SH) that have significant difference (p<0.05) with OVX group and AD-1 group, but there was no significant difference with AD-2 and AD-3 (p>0,05). In conclusion, honey (Apis dorsata) supplements has the effect of increasing bone strength in ovariectomized rat as animal models of osteoporosis, so that honey (Apis dorsata) supplements has the potential to be used as an alternative treatment for osteoporosis.

Web based tools for visualizing imaging data and development of XNATView, a zero footprint image viewer

PubMed Central

Gutman, David A.; Dunn, William D.; Cobb, Jake; Stoner, Richard M.; Kalpathy-Cramer, Jayashree; Erickson, Bradley

2014-01-01

Advances in web technologies now allow direct visualization of imaging data sets without necessitating the download of large file sets or the installation of software. This allows centralization of file storage and facilitates image review and analysis. XNATView is a light framework recently developed in our lab to visualize DICOM images stored in The Extensible Neuroimaging Archive Toolkit (XNAT). It consists of a PyXNAT-based framework to wrap around the REST application programming interface (API) and query the data in XNAT. XNATView was developed to simplify quality assurance, help organize imaging data, and facilitate data sharing for intra- and inter-laboratory collaborations. Its zero-footprint design allows the user to connect to XNAT from a web browser, navigate through projects, experiments, and subjects, and view DICOM images with accompanying metadata all within a single viewing instance. PMID:24904399

In Vitro and In Vivo Characterization of Drug Nanoparticles Prepared Using PureNano™ Continuous Crystallizer to Improve the Bioavailability of Poorly Water Soluble Drugs.

PubMed

Tahara, Kohei; Nishikawa, Masahiro; Matsui, Ko; Hisazumi, Koji; Onodera, Risako; Tozuka, Yuichi; Takeuchi, Hirofumi

2016-09-01

The aim of this study was to enhance the dissolution and oral absorption of poorly water-soluble active pharmaceutical ingredients (APIs) using nanoparticle suspensions prepared with a PureNano™ continuous crystallizer (PCC). Nanoparticle suspensions were prepared with a PCC, which is based on microfluidics reaction technology and solvent-antisolvent crystallization. Phenytoin, bezafibrate, flurbiprofen, and miconazole were used as model APIs. These APIs were dissolved in ethanol and precipitated by the addition of water and polyvinyl alcohol. Batch crystallization (BC) using a beaker was also performed to prepare the suspensions. Both PCC and BC formulations were freeze-dried before being characterized in vitro and in vivo. The particle sizes of the nanoparticle suspensions prepared with the PCC were smaller than those prepared by BC. The dissolution rate of each API in vitro significantly increased after crystallization. Reducing the particle size of either the BC or PCC formulation led to increased API flux across Caco-2 cell monolayers. PCC preparations showed higher plasma concentrations after oral administration, demonstrating the advantages of a fast dissolution rate and increased interaction with the gastrointestinal tract owing to the smaller particle size. PCC can continuously produce nanoparticle APIs and is an efficient approach for improving their oral bioavailability.

An adaptive software defined radio design based on a standard space telecommunication radio system API

NASA Astrophysics Data System (ADS)

Xiong, Wenhao; Tian, Xin; Chen, Genshe; Pham, Khanh; Blasch, Erik

2017-05-01

Software defined radio (SDR) has become a popular tool for the implementation and testing for communications performance. The advantage of the SDR approach includes: a re-configurable design, adaptive response to changing conditions, efficient development, and highly versatile implementation. In order to understand the benefits of SDR, the space telecommunication radio system (STRS) was proposed by NASA Glenn research center (GRC) along with the standard application program interface (API) structure. Each component of the system uses a well-defined API to communicate with other components. The benefit of standard API is to relax the platform limitation of each component for addition options. For example, the waveform generating process can support a field programmable gate array (FPGA), personal computer (PC), or an embedded system. As long as the API defines the requirements, the generated waveform selection will work with the complete system. In this paper, we demonstrate the design and development of adaptive SDR following the STRS and standard API protocol. We introduce step by step the SDR testbed system including the controlling graphic user interface (GUI), database, GNU radio hardware control, and universal software radio peripheral (USRP) tranceiving front end. In addition, a performance evaluation in shown on the effectiveness of the SDR approach for space telecommunication.

Influence of formulation and processing factors on stability of levothyroxine sodium pentahydrate.

PubMed

Collier, Jarrod W; Shah, Rakhi B; Gupta, Abhay; Sayeed, Vilayat; Habib, Muhammad J; Khan, Mansoor A

2010-06-01

Stability of formulations over shelf-life is critical for having a quality product. Choice of excipients, manufacturing process, storage conditions, and packaging can either mitigate or enhance the degradation of the active pharmaceutical ingredient (API), affecting potency and/or stability. The purpose was to investigate the influence of processing and formulation factors on stability of levothyroxine (API). The API was stored at long-term (25 degrees C/60%RH), accelerated (40 degrees C/75%RH), and low-humidity (25 degrees C/0%RH and 40 degrees C/0%RH) conditions for 28 days. Effect of moisture loss was evaluated by drying it (room temperature, N(2)) and placed at 25 degrees C/0%RH and 40 degrees C/0%RH. The API was incubated with various excipients (based on package insert of marketed tablets) in either 1:1, 1:10, or 1:100 ratios with 5% moisture at 60 degrees C. Commonly used ratios for excipients were used. The equilibrium sorption data was collected on the API and excipients. The API was stable in solid state for the study duration under all conditions for both forms (potency between 90% and 110%). Excipients effect on stability varied and crospovidone, povidone, and sodium laurel sulfate (SLS) caused significant API degradation where deiodination and deamination occurred. Moisture sorption values were different across excipients. Crospovidone and povidone were hygroscopic whereas SLS showed deliquescence at high RH. The transient formulation procedures where temperature might go up or humidity might go down would not have major impact on the API stability. Excipients influence stability and if possible, those three should either be avoided or used in minimum quantity which could provide more stable tablet formulations with minimum potency loss throughout its shelf-life.

Rheology Guided Rational Selection of Processing Temperature To Prepare Copovidone-Nifedipine Amorphous Solid Dispersions via Hot Melt Extrusion (HME).

PubMed

Yang, Fengyuan; Su, Yongchao; Zhang, Jingtao; DiNunzio, James; Leone, Anthony; Huang, Chengbin; Brown, Chad D

2016-10-03

The production of amorphous solid dispersions via hot melt extrusion (HME) relies on elevated temperature and prolonged residence time, which can result in potential degradation and decomposition of thermally sensitive components. Herein, the rheological properties of a physical mixture of polymer and an active pharmaceutical ingredient (API) were utilized to guide the selection of appropriate HME processing temperature. In the currently studied copovidone-nifedipine system, a critical temperature, which is substantially lower (∼13 °C) than the melting point of crystalline API, was captured during a temperature ramp examination and regarded as the critical point at which the API could molecularly dissolve into the polymer. Based on the identification of this critical point, various solid dispersions were prepared by HME processing below, at, and above the critical temperature (both below and above the melting temperature (T m ) of crystalline API). In addition, the resultant extrudates along with two control solid dispersions prepared by physical mixing and cryogenic milling were assessed by X-ray diffraction, differential scanning calorimetry, hot stage microscopy, rheology, and solid-state NMR. Physicochemical properties of resultant solid dispersions indicated that the identified critical temperature is sufficient for the polymer-API system to reach a molecular-level mixing, manifested by the transparent and smooth appearance of extrudates, the absence of API crystalline diffraction and melting peaks, dramatically decreased rheological properties, and significantly improved polymer-API miscibility. Once the critical temperature has been achieved, further raising the processing temperature only results in limited improvement of API dispersion, reflected by slightly reduced storage modulus and complex viscosity and limited improvement in miscibility.

A RESTful API for accessing microbial community data for MG-RAST

DOE PAGES

Wilke, Andreas; Bischof, Jared; Harrison, Travis; ...

2015-01-08

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MGRAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, asmore » well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http:// kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase’s microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service.« less

The development, validity, and reliability of the Addiction Profile Index (API).

PubMed

Ögel, Kültegin; Evren, Cüneyt; Karadağ, Figen; Gürol, Defne Tamar

2012-01-01

The objective of this study was to develop a practical questionnaire for multidimensional assessment of problems associated with alcohol and substance abuse that would also be useful for treatment planning. The Addiction Profile Index (API) is a self-report questionnaire consisting of 37 items and the following 5 subscales: characteristics of substance use; dependency diagnosis; the effects of subsance use on the user; craving; motivation to quit using substances. The study included 345 alcohol and/or substance abusers from 2 addiction treatment clinics and a prison addiction service. The validity of the questionnaire was assessed using the Michigan Alcoholism Screening Test (MAST), Readiness to Change Questionnaire (SOCRATES), Penn Alcohol Craving Scale (PACS), Drug Craving Scale (DCS), Structured Clinical Interview for DSM-IV Axis I Disorders (SCID-I), and Addiction Severity Index (ASI). The Cronbach's alpha coefficient for the total API was 0.89 and for the subscales it ranged from 0.63 to 0.86. Item-total correlation coefficients ranged from 0.42 to 0.89. The Spearman Brown split-half method coefficient for the total API was 0.83. In all, 4 factors were obtained using explanatory factor analysis that represented 52.3% of the total variance. The API craving subscale was observed to be consistent with PACS and the API motivation subscale was consistent with SOCRATES. The API total score was strongly correlated with the mean MAST score, and the composite ASI medical status, substance use, legal status, and family social relations subscale scores. Based on ROC analyses, the area under curve was 0.90. With a total API cut-off score of 4, the scale's sensitivity and specificity 0.85 was 0.78, respectively. The findings show that the API is a valid and reliable questionnaire that can be used to measure the severity of different dimensions of substance dependency.

A RESTful API for Accessing Microbial Community Data for MG-RAST

PubMed Central

Wilke, Andreas; Bischof, Jared; Harrison, Travis; Brettin, Tom; D'Souza, Mark; Gerlach, Wolfgang; Matthews, Hunter; Paczian, Tobias; Wilkening, Jared; Glass, Elizabeth M.; Desai, Narayan; Meyer, Folker

2015-01-01

Metagenomic sequencing has produced significant amounts of data in recent years. For example, as of summer 2013, MG-RAST has been used to annotate over 110,000 data sets totaling over 43 Terabases. With metagenomic sequencing finding even wider adoption in the scientific community, the existing web-based analysis tools and infrastructure in MG-RAST provide limited capability for data retrieval and analysis, such as comparative analysis between multiple data sets. Moreover, although the system provides many analysis tools, it is not comprehensive. By opening MG-RAST up via a web services API (application programmers interface) we have greatly expanded access to MG-RAST data, as well as provided a mechanism for the use of third-party analysis tools with MG-RAST data. This RESTful API makes all data and data objects created by the MG-RAST pipeline accessible as JSON objects. As part of the DOE Systems Biology Knowledgebase project (KBase, http://kbase.us) we have implemented a web services API for MG-RAST. This API complements the existing MG-RAST web interface and constitutes the basis of KBase's microbial community capabilities. In addition, the API exposes a comprehensive collection of data to programmers. This API, which uses a RESTful (Representational State Transfer) implementation, is compatible with most programming environments and should be easy to use for end users and third parties. It provides comprehensive access to sequence data, quality control results, annotations, and many other data types. Where feasible, we have used standards to expose data and metadata. Code examples are provided in a number of languages both to show the versatility of the API and to provide a starting point for users. We present an API that exposes the data in MG-RAST for consumption by our users, greatly enhancing the utility of the MG-RAST service. PMID:25569221

Cocrystal solubility product analysis - Dual concentration-pH mass action model not dependent on explicit solubility equations.

PubMed

Avdeef, Alex

2017-12-15

A novel general computational approach is described to address many aspects of cocrystal (CC) solubility product (K sp ) determination of drug substances. The CC analysis program, pDISOL-X, was developed and validated with published model systems of various acid-base combinations of active pharmaceutical ingredients (APIs) and coformers: (i) carbamazepine cocrystal systems with 4-aminobenzoic acid, cinnamic acid, saccharin, and salicylic acid, (ii) for indomethacin with saccharin, (iii) for nevirapine with maleic acid, saccharin, and salicylic acid, and (iv) for gabapentin with 3-hydroxybenzoic acid. In all systems but gabapentin, the coformer is much more soluble than the API. The model systems selected are those with available published dual concentration-pH data, one set for the API and one set for the coformer, generally measured at eutectic points (thermodynamically-stable three phases: solution, cocrystal, and crystalline API or coformer). The carbamazepine-cinnamic acid CC showed a substantial elevation in the API equilibrium concentration above pH5, consistent with the formation of a complex between carbamazepine and cinnamate anion. The analysis of the gabapentin:3-hydroxybenzoic acid 1:1 CC system indicated four zones of solid suspensions: coformer (pH<3.25), coformer and cocrystal eutectic (pH3.25-4.44), cocrystal (pH4.44-5.62), and API (pH>5.62). The general approach allows for testing of many possible equilibrium models, including those comprising drug-coformer complexation. The program calculates the ionic strength at each pH. From this, the equilibrium constants are adjusted for activity effects, based on the Stokes-Robinson hydration theory. The complete speciation analysis of the CC systems may provide useful insights into pH-sensitive dissolution effects that could potentially influence bioavailability. Copyright © 2017 Elsevier B.V. All rights reserved.

Dropwise additive manufacturing of pharmaceutical products for solvent-based dosage forms.

PubMed

Hirshfield, Laura; Giridhar, Arun; Taylor, Lynne S; Harris, Michael T; Reklaitis, Gintaras V

2014-02-01

In recent years, the US Food and Drug Administration has encouraged pharmaceutical companies to develop more innovative and efficient manufacturing methods with improved online monitoring and control. Mini-manufacturing of medicine is one such method enabling the creation of individualized product forms for each patient. This work presents dropwise additive manufacturing of pharmaceutical products (DAMPP), an automated, controlled mini-manufacturing method that deposits active pharmaceutical ingredients (APIs) directly onto edible substrates using drop-on-demand (DoD) inkjet printing technology. The use of DoD technology allows for precise control over the material properties, drug solid state form, drop size, and drop dynamics and can be beneficial in the creation of high-potency drug forms, combination drugs with multiple APIs or individualized medicine products tailored to a specific patient. In this work, DAMPP was used to create dosage forms from solvent-based formulations consisting of API, polymer, and solvent carrier. The forms were then analyzed to determine the reproducibility of creating an on-target dosage form, the morphology of the API of the final form and the dissolution behavior of the drug over time. DAMPP is found to be a viable alternative to traditional mass-manufacturing methods for solvent-based oral dosage forms. © 2013 Wiley Periodicals, Inc. and the American Pharmacists Association.

The application of structure-based assessment to support safety and chemistry diligence to manage genotoxic impurities in active pharmaceutical ingredients during drug development.

PubMed

Dobo, Krista L; Greene, Nigel; Cyr, Michelle O; Caron, Stéphane; Ku, Warren W

2006-04-01

Starting materials and intermediates used to synthesize pharmaceuticals are reactive in nature and may be present as impurities in the active pharmaceutical ingredient (API) used for preclinical safety studies and clinical trials. Furthermore, starting materials and intermediates may be known or suspected mutagens and/or carcinogens. Therefore, during drug development due diligence need be applied from two perspectives (1) to understand potential mutagenic and carcinogenic risks associated with compounds used for synthesis and (2) to understand the capability of synthetic processes to control genotoxic impurities in the API. Recently, a task force comprised of experts from pharmaceutical industry proposed guidance, with recommendations for classification, testing, qualification and assessing risk of genotoxic impurities. In our experience the proposed structure-based classification, has differentiated 75% of starting materials and intermediates as mutagenic and non-mutagenic with high concordance (92%) when compared with Ames results. Structure-based assessment has been used to identify genotoxic hazards, and prompted evaluation of fate of genotoxic impurities in API. These two assessments (safety and chemistry) culminate in identification of genotoxic impurities known or suspected to exceed acceptable levels in API, thereby triggering actions needed to assure appropriate control and measurement methods are in place. Hypothetical case studies are presented demonstrating this multi-disciplinary approach.

Sensing the intruder: a quantitative threshold for recognition cues perception in honeybees

NASA Astrophysics Data System (ADS)

Cappa, Federico; Bruschini, Claudia; Cipollini, Maria; Pieraccini, Giuseppe; Cervo, Rita

2014-02-01

The ability to discriminate among nestmates and non-nestmate is essential to defend social insect colonies from intruders. Over the years, nestmate recognition has been extensively studied in the honeybee Apis mellifera; nevertheless, the quantitative perceptual aspects at the basis of the recognition system represent an unexplored subject in this species. To test the existence of a cuticular hydrocarbons' quantitative perception threshold for nestmate recognition cues, we conducted behavioural assays by presenting different amounts of a foreign forager's chemical profile to honeybees at the entrance of their colonies. We found an increase in the explorative and aggressive responses as the amount of cues increased based on a threshold mechanism, highlighting the importance of the quantitative perceptual features for the recognition processes in A. mellifera.

Lab Streaming Layer Enabled Myo Data Collection Software User Manual

DTIC Science & Technology

2017-06-07

time - series data over a local network. LSL handles the networking, time -synchronization, (near-) real- time access as well as, optionally, the... series data collection (e.g., brain activity, heart activity, muscle activity) using the LSL application programming interface (API). Time -synchronized...saved to a single extensible data format (XDF) file. Once the time - series data are collected in a Lab Recorder XDF file, users will be able to query

The Human-Robot Interaction Operating System

NASA Technical Reports Server (NTRS)

Fong, Terrence; Kunz, Clayton; Hiatt, Laura M.; Bugajska, Magda

2006-01-01

In order for humans and robots to work effectively together, they need to be able to converse about abilities, goals and achievements. Thus, we are developing an interaction infrastructure called the "Human-Robot Interaction Operating System" (HRI/OS). The HRI/OS provides a structured software framework for building human-robot teams, supports a variety of user interfaces, enables humans and robots to engage in task-oriented dialogue, and facilitates integration of robots through an extensible API.

Leveraging OpenStudio's Application Programming Interfaces: Preprint

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

Long, N.; Ball, B.; Goldwasser, D.

2013-11-01

OpenStudio development efforts have been focused on providing Application Programming Interfaces (APIs) where users are able to extend OpenStudio without the need to compile the open source libraries. This paper will discuss the basic purposes and functionalities of the core libraries that have been wrapped with APIs including the Building Model, Results Processing, Advanced Analysis, UncertaintyQuantification, and Data Interoperability through Translators. Several building energy modeling applications have been produced using OpenStudio's API and Software Development Kits (SDK) including the United States Department of Energy's Asset ScoreCalculator, a mobile-based audit tool, an energy design assistance reporting protocol, and a portfolio scalemore » incentive optimization analysismethodology. Each of these software applications will be discussed briefly and will describe how the APIs were leveraged for various uses including high-level modeling, data transformations from detailed building audits, error checking/quality assurance of models, and use of high-performance computing for mass simulations.« less

Component-resolved diagnosis in hymenoptera allergy.

PubMed

Antolín-Amérigo, D; Ruiz-León, B; Boni, E; Alfaya-Arias, T; Álvarez-Mon, M; Barbarroja-Escudero, J; González-de-Olano, D; Moreno-Aguilar, C; Rodríguez-Rodríguez, M; Sánchez-González, M J; Sánchez-Morillas, L; Vega-Castro, A

Component-resolved diagnosis based on the use of well-defined, properly characterised and purified natural and recombinant allergens constitutes a new approach in the diagnosis of venom allergy. Prospective readers may benefit from an up-to-date review on the allergens. The best characterised venom is that of Apis mellifera, whose main allergens are phospholipase A2 (Api m1), hyaluronidase (Api m2) and melittin (Api m4). Additionally, in recent years, new allergens of Vespula vulgaris have been identified and include phospholipase A1 (Ves v1), hyaluronidase (Ves v2) and antigen 5 (Ves v5). Polistes species are becoming an increasing cause of allergy in Europe, although only few allergens have been identified in this venom. In this review, we evaluate the current knowledge about molecular diagnosis in hymenoptera venom allergy. Copyright © 2017 SEICAP. Published by Elsevier España, S.L.U. All rights reserved.

[Evaluation of common commercial systems for the identification of yeast isolates in microbiology laboratories: a multicenter study].

PubMed

Karabıçak, Nilgün; Uludağ Altun, Hatice; Karatuna, Onur; Hazırolan, Gülşen; Aksu, Neriman; Adiloğlu, Ali; Akyar, Işın

2015-04-01

Accurate and rapid identification of yeast isolates have become important in recent years for not only antifungal susceptibility testing due to the species-specific clinical resistance breakpoints but also early initiation of appropriate antifungal therapy. In clinical microbiology laboratories species identification of yeasts is often performed with several commercial systems based on biochemical properties and rarely according to the physiological and morphological characteristics. The aim of this study was to compare the two common commercial systems, VITEK 2 YST ID Card (Vitek; bioMérieux, France) and API 20C AUX (API; bioMérieux, France) with conventional mycological methods. A total of 473 clinical yeast strains isolated from clinical specimens in different university and training/research hospitals and identified by Vitek system were included in the study. The isolates were re-identified with API and conventional methods including morphological identification in the Mycology Reference Laboratory of the Public Health Institute of Turkey. Candida dubliniensis MYA 583, Candida krusei ATCC 6258, Candida parapsilosis ATCC 22019, Candida albicans ATCC 10231 and Cryptococcus neoformans ATCC 32268 were used as quality control strains and those standard strains were studied consecutively 10 days with both of the methods. The results of identification by Vitek and API were compared with the results of conventional methods for those 473 yeast isolates [6 genus (Candida, Cryptococcus, Blastoshizomyces, Rhodotorula, Saccharomyces, Trichosporon), 17 species (5 common and 12 rarely isolated)]. The performances of the systems were better (Vitek: 95%; API: 96%) for the commonly detected species (C.albicans, C.parapsilosis, C.glabrata, C.tropicalis and C.krusei) than those for rarely detected species (Vitek: 78.4%; API: 71.6%) (p= 0.155). Misidentification or unidentification were mostly detected for C.parapsilosis (Vitek: 6/87; API: 7/87) and C.glabrata (Vitek: 9/104; API: 3/104) by both of the systems. For rarely detected yeast isolates, misidentification or unidentification were most frequently observed in species of C.pelliculosa (Vitek: 3/11; API: 6/11) and C.dubliniensis (API and Vitek: 2/5) isolates. Candida guilliermondii (API: 2/5) isolates had lower rate of identification with API compared to other species. Blastoschizomyces capitatus and Saccharomyces cerevisiae isolates could not be identified by both of the systems. As a result, the accurate diagnosis of Vitek and API systems were similar in terms of consistency (86.3%). Two systems performed well in correct identification of common clinical yeast species (at least 95%), while the identification of rare species was more challenging indicating that they require further morphological and physiological testing. The addition of morphological identification to commercial systems will be useful for accurate diagnosis and treatment of mixed infections.

Comparative Sucrose Responsiveness in Apis mellifera and A. cerana Foragers

PubMed Central

Yang, Wenchao; Kuang, Haiou; Wang, Shanshan; Wang, Jie; Liu, Wei; Wu, Zhenhong; Tian, Yuanyuan; Huang, Zachary Y.; Miao, Xiaoqing

2013-01-01

In the European honey bee, Apis mellifera, pollen foragers have a higher sucrose responsiveness than nectar foragers when tested using a proboscis extension response (PER) assay. In addition, Africanized honey bees have a higher sucrose responsiveness than European honey bees. Based on the biology of the Eastern honey bee, A. cerana, we hypothesized that A. cerana should also have a higher responsiveness to sucrose than A. mellifera. To test this hypothesis, we compared the sucrose thresholds of pollen foragers and nectar foragers in both A. cerana and A. mellifera in Fujian Province, China. Pollen foragers were more responsive to sucrose than nectar foragers in both species, consistent with previous studies. However, contrary to our hypothesis, A. mellifera was more responsive than A. cerana. We also demonstrated that this higher sucrose responsiveness in A. mellifera was not due to differences in the colony environment by co-fostering two species of bees in the same mixed-species colonies. Because A. mellifera foragers were more responsive to sucrose, we predicted that their nectar foragers should bring in less concentrated nectar compared to that of A. cerana. However, we found no differences between the two species. We conclude that A. cerana shows a different pattern in sucrose responsiveness from that of Africanized bees. There may be other mechanisms that enable A. cerana to perform well in areas with sparse nectar resources. PMID:24194958

Viral infection affects sucrose responsiveness and homing ability of forager honey bees, Apis mellifera L.

PubMed

Li, Zhiguo; Chen, Yanping; Zhang, Shaowu; Chen, Shenglu; Li, Wenfeng; Yan, Limin; Shi, Liangen; Wu, Lyman; Sohr, Alex; Su, Songkun

2013-01-01

Honey bee health is mainly affected by Varroa destructor, viruses, Nosema spp., pesticide residues and poor nutrition. Interactions between these proposed factors may be responsible for the colony losses reported worldwide in recent years. In the present study, the effects of a honey bee virus, Israeli acute paralysis virus (IAPV), on the foraging behaviors and homing ability of European honey bees (Apis mellifera L.) were investigated based on proboscis extension response (PER) assays and radio frequency identification (RFID) systems. The pollen forager honey bees originated from colonies that had no detectable level of honey bee viruses and were manually inoculated with IAPV to induce the viral infection. The results showed that IAPV-inoculated honey bees were more responsive to low sucrose solutions compared to that of non-infected foragers. After two days of infection, around 10⁷ copies of IAPV were detected in the heads of these honey bees. The homing ability of IAPV-infected foragers was depressed significantly in comparison to the homing ability of uninfected foragers. The data provided evidence that IAPV infection in the heads may enable the virus to disorder foraging roles of honey bees and to interfere with brain functions that are responsible for learning, navigation, and orientation in the honey bees, thus, making honey bees have a lower response threshold to sucrose and lose their way back to the hive.

Viral Infection Affects Sucrose Responsiveness and Homing Ability of Forager Honey Bees, Apis mellifera L.

PubMed Central

Li, Zhiguo; Chen, Yanping; Zhang, Shaowu; Chen, Shenglu; Li, Wenfeng; Yan, Limin; Shi, Liangen; Wu, Lyman; Sohr, Alex; Su, Songkun

2013-01-01

Honey bee health is mainly affected by Varroa destructor, viruses, Nosema spp., pesticide residues and poor nutrition. Interactions between these proposed factors may be responsible for the colony losses reported worldwide in recent years. In the present study, the effects of a honey bee virus, Israeli acute paralysis virus (IAPV), on the foraging behaviors and homing ability of European honey bees (Apis mellifera L.) were investigated based on proboscis extension response (PER) assays and radio frequency identification (RFID) systems. The pollen forager honey bees originated from colonies that had no detectable level of honey bee viruses and were manually inoculated with IAPV to induce the viral infection. The results showed that IAPV-inoculated honey bees were more responsive to low sucrose solutions compared to that of non-infected foragers. After two days of infection, around 107 copies of IAPV were detected in the heads of these honey bees. The homing ability of IAPV-infected foragers was depressed significantly in comparison to the homing ability of uninfected foragers. The data provided evidence that IAPV infection in the heads may enable the virus to disorder foraging roles of honey bees and to interfere with brain functions that are responsible for learning, navigation, and orientation in the honey bees, thus, making honey bees have a lower response threshold to sucrose and lose their way back to the hive. PMID:24130876

Comparative sucrose responsiveness in Apis mellifera and A. cerana foragers.

PubMed

Yang, Wenchao; Kuang, Haiou; Wang, Shanshan; Wang, Jie; Liu, Wei; Wu, Zhenhong; Tian, Yuanyuan; Huang, Zachary Y; Miao, Xiaoqing

2013-01-01

In the European honey bee, Apis mellifera, pollen foragers have a higher sucrose responsiveness than nectar foragers when tested using a proboscis extension response (PER) assay. In addition, Africanized honey bees have a higher sucrose responsiveness than European honey bees. Based on the biology of the Eastern honey bee, A. cerana, we hypothesized that A. cerana should also have a higher responsiveness to sucrose than A. mellifera. To test this hypothesis, we compared the sucrose thresholds of pollen foragers and nectar foragers in both A. cerana and A. mellifera in Fujian Province, China. Pollen foragers were more responsive to sucrose than nectar foragers in both species, consistent with previous studies. However, contrary to our hypothesis, A. mellifera was more responsive than A. cerana. We also demonstrated that this higher sucrose responsiveness in A. mellifera was not due to differences in the colony environment by co-fostering two species of bees in the same mixed-species colonies. Because A. mellifera foragers were more responsive to sucrose, we predicted that their nectar foragers should bring in less concentrated nectar compared to that of A. cerana. However, we found no differences between the two species. We conclude that A. cerana shows a different pattern in sucrose responsiveness from that of Africanized bees. There may be other mechanisms that enable A. cerana to perform well in areas with sparse nectar resources.

OpenMSI: A High-Performance Web-Based Platform for Mass Spectrometry Imaging

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

Rubel, Oliver; Greiner, Annette; Cholia, Shreyas

Mass spectrometry imaging (MSI) enables researchers to directly probe endogenous molecules directly within the architecture of the biological matrix. Unfortunately, efficient access, management, and analysis of the data generated by MSI approaches remain major challenges to this rapidly developing field. Despite the availability of numerous dedicated file formats and software packages, it is a widely held viewpoint that the biggest challenge is simply opening, sharing, and analyzing a file without loss of information. Here we present OpenMSI, a software framework and platform that addresses these challenges via an advanced, high-performance, extensible file format and Web API for remote data accessmore » (http://openmsi.nersc.gov). The OpenMSI file format supports storage of raw MSI data, metadata, and derived analyses in a single, self-describing format based on HDF5 and is supported by a large range of analysis software (e.g., Matlab and R) and programming languages (e.g., C++, Fortran, and Python). Careful optimization of the storage layout of MSI data sets using chunking, compression, and data replication accelerates common, selective data access operations while minimizing data storage requirements and are critical enablers of rapid data I/O. The OpenMSI file format has shown to provide >2000-fold improvement for image access operations, enabling spectrum and image retrieval in less than 0.3 s across the Internet even for 50 GB MSI data sets. To make remote high-performance compute resources accessible for analysis and to facilitate data sharing and collaboration, we describe an easy-to-use yet powerful Web API, enabling fast and convenient access to MSI data, metadata, and derived analysis results stored remotely to facilitate high-performance data analysis and enable implementation of Web based data sharing, visualization, and analysis.« less

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

David Lawrence

Calibrations and conditions databases can be accessed from within the JANA Event Processing framework through the API defined in its JCalibration base class. The API is designed to support everything from databases, to web services to flat files for the backend. A Web Service backend using the gSOAP toolkit has been implemented which is particularly interesting since it addresses many modern cybersecurity issues including support for SSL. The API allows constants to be retrieved through a single line of C++ code with most of the context, including the transport mechanism, being implied by the run currently being analyzed and themore » environment relieving developers from implementing such details.« less

The eNanoMapper database for nanomaterial safety information

PubMed Central

Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

Summary Background: The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. Results: The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. Conclusion: We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the “representational state transfer” (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure–activity relationships for nanomaterials (NanoQSAR). PMID:26425413

The eNanoMapper database for nanomaterial safety information.

PubMed

Jeliazkova, Nina; Chomenidis, Charalampos; Doganis, Philip; Fadeel, Bengt; Grafström, Roland; Hardy, Barry; Hastings, Janna; Hegi, Markus; Jeliazkov, Vedrin; Kochev, Nikolay; Kohonen, Pekka; Munteanu, Cristian R; Sarimveis, Haralambos; Smeets, Bart; Sopasakis, Pantelis; Tsiliki, Georgia; Vorgrimmler, David; Willighagen, Egon

2015-01-01

The NanoSafety Cluster, a cluster of projects funded by the European Commision, identified the need for a computational infrastructure for toxicological data management of engineered nanomaterials (ENMs). Ontologies, open standards, and interoperable designs were envisioned to empower a harmonized approach to European research in nanotechnology. This setting provides a number of opportunities and challenges in the representation of nanomaterials data and the integration of ENM information originating from diverse systems. Within this cluster, eNanoMapper works towards supporting the collaborative safety assessment for ENMs by creating a modular and extensible infrastructure for data sharing, data analysis, and building computational toxicology models for ENMs. The eNanoMapper database solution builds on the previous experience of the consortium partners in supporting diverse data through flexible data storage, open source components and web services. We have recently described the design of the eNanoMapper prototype database along with a summary of challenges in the representation of ENM data and an extensive review of existing nano-related data models, databases, and nanomaterials-related entries in chemical and toxicogenomic databases. This paper continues with a focus on the database functionality exposed through its application programming interface (API), and its use in visualisation and modelling. Considering the preferred community practice of using spreadsheet templates, we developed a configurable spreadsheet parser facilitating user friendly data preparation and data upload. We further present a web application able to retrieve the experimental data via the API and analyze it with multiple data preprocessing and machine learning algorithms. We demonstrate how the eNanoMapper database is used to import and publish online ENM and assay data from several data sources, how the "representational state transfer" (REST) API enables building user friendly interfaces and graphical summaries of the data, and how these resources facilitate the modelling of reproducible quantitative structure-activity relationships for nanomaterials (NanoQSAR).

Similar English Learner Students, Different Results: Why Do Some Schools Do Better? A Follow-Up Analysis, Based upon a Large-Scale Survey of California Elementary Schools Serving High Proportions of Low-Income and EL Students. Research Brief

ERIC Educational Resources Information Center

Williams, Trish; Perry, Mary; Oregon, Isabel; Brazil, Noli; Hakuta, Kenji; Haertel, Edward; Kirst, Michael; Levin, Jesse

2007-01-01

In spring 2006 California released its first ever school-level Academic Performance Index (API) scores for English Learners (ELs). These EL-API scores were based on California Standards Tests taken in the spring of 2005, and make it possible to identify how well schools were doing with this student population. It is not unexpected that elementary…

Allergenic relevance of nonspecific lipid transfer proteins 2: Identification and characterization of Api g 6 from celery tuber as representative of a novel IgE-binding protein family.

PubMed

Vejvar, Eva; Himly, Martin; Briza, Peter; Eichhorn, Stephanie; Ebner, Christof; Hemmer, Wolfgang; Ferreira, Fatima; Gadermaier, Gabriele

2013-11-01

Apium graveolens represents a relevant food allergen source linked with severe systemic reactions. We sought to identify an IgE-binding nonspecific lipid transfer protein (nsLTP) in celery tuber. A low molecular weight protein exclusively present in celery tuber was purified and designated Api g 6. The entire protein sequence was obtained by MS and classified as member of the nsLTP2 family. Api g 6 is monomeric in solution with a molecular mass of 6936 Da. The alpha-helical disulfide bond-stabilized structure confers tremendous thermal stability (Tm > 90°C) and high resistance to gastrointestinal digestion. Endolysosomal degradation demonstrated low susceptibility and the presence of a dominant peptide cluster at the C-terminus. Thirty-eight percent of A. graveolens allergic patients demonstrated IgE reactivity to purified natural Api g 6 in ELISA and heat treatment did only partially reduce its allergenic activity. No correlation in IgE binding and limited cross-reactivity was observed with Api g 2 and Art v 3, nsLTP1 from celery stalks and mugwort pollen. Api g 6, a novel nsLTP2 from celery tuber represents the first well-characterized allergen in this protein family. Despite similar structural and physicochemical features as nsLTP1, immunological properties of Api g 6 are distinct which warrants its inclusion in molecule-based diagnosis of A. graveolens allergy. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Movement Analysis of Flexion and Extension of Honeybee Abdomen Based on an Adaptive Segmented Structure

PubMed Central

Zhao, Jieliang; Wu, Jianing; Yan, Shaoze

2015-01-01

Honeybees (Apis mellifera) curl their abdomens for daily rhythmic activities. Prior to determining this fact, people have concluded that honeybees could curl their abdomen casually. However, an intriguing but less studied feature is the possible unidirectional abdominal deformation in free-flying honeybees. A high-speed video camera was used to capture the curling and to analyze the changes in the arc length of the honeybee abdomen not only in free-flying mode but also in the fixed sample. Frozen sections and environment scanning electron microscope were used to investigate the microstructure and motion principle of honeybee abdomen and to explore the physical structure restricting its curling. An adaptive segmented structure, especially the folded intersegmental membrane (FIM), plays a dominant role in the flexion and extension of the abdomen. The structural features of FIM were utilized to mimic and exhibit movement restriction on honeybee abdomen. Combining experimental analysis and theoretical demonstration, a unidirectional bending mechanism of honeybee abdomen was revealed. Through this finding, a new perspective for aerospace vehicle design can be imitated. PMID:26223946

The Open Microscopy Environment: open image informatics for the biological sciences

NASA Astrophysics Data System (ADS)

Blackburn, Colin; Allan, Chris; Besson, Sébastien; Burel, Jean-Marie; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gault, David; Gillen, Kenneth; Leigh, Roger; Leo, Simone; Li, Simon; Lindner, Dominik; Linkert, Melissa; Moore, Josh; Moore, William J.; Ramalingam, Balaji; Rozbicki, Emil; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Swedlow, Jason R.

2016-07-01

Despite significant advances in biological imaging and analysis, major informatics challenges remain unsolved: file formats are proprietary, storage and analysis facilities are lacking, as are standards for sharing image data and results. While the open FITS file format is ubiquitous in astronomy, astronomical imaging shares many challenges with biological imaging, including the need to share large image sets using secure, cross-platform APIs, and the need for scalable applications for processing and visualization. The Open Microscopy Environment (OME) is an open-source software framework developed to address these challenges. OME tools include: an open data model for multidimensional imaging (OME Data Model); an open file format (OME-TIFF) and library (Bio-Formats) enabling free access to images (5D+) written in more than 145 formats from many imaging domains, including FITS; and a data management server (OMERO). The Java-based OMERO client-server platform comprises an image metadata store, an image repository, visualization and analysis by remote access, allowing sharing and publishing of image data. OMERO provides a means to manage the data through a multi-platform API. OMERO's model-based architecture has enabled its extension into a range of imaging domains, including light and electron microscopy, high content screening, digital pathology and recently into applications using non-image data from clinical and genomic studies. This is made possible using the Bio-Formats library. The current release includes a single mechanism for accessing image data of all types, regardless of original file format, via Java, C/C++ and Python and a variety of applications and environments (e.g. ImageJ, Matlab and R).

SU-F-J-94: Development of a Plug-in Based Image Analysis Tool for Integration Into Treatment Planning

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

Owen, D; Anderson, C; Mayo, C

Purpose: To extend the functionality of a commercial treatment planning system (TPS) to support (i) direct use of quantitative image-based metrics within treatment plan optimization and (ii) evaluation of dose-functional volume relationships to assist in functional image adaptive radiotherapy. Methods: A script was written that interfaces with a commercial TPS via an Application Programming Interface (API). The script executes a program that performs dose-functional volume analyses. Written in C#, the script reads the dose grid and correlates it with image data on a voxel-by-voxel basis through API extensions that can access registration transforms. A user interface was designed through WinFormsmore » to input parameters and display results. To test the performance of this program, image- and dose-based metrics computed from perfusion SPECT images aligned to the treatment planning CT were generated, validated, and compared. Results: The integration of image analysis information was successfully implemented as a plug-in to a commercial TPS. Perfusion SPECT images were used to validate the calculation and display of image-based metrics as well as dose-intensity metrics and histograms for defined structures on the treatment planning CT. Various biological dose correction models, custom image-based metrics, dose-intensity computations, and dose-intensity histograms were applied to analyze the image-dose profile. Conclusion: It is possible to add image analysis features to commercial TPSs through custom scripting applications. A tool was developed to enable the evaluation of image-intensity-based metrics in the context of functional targeting and avoidance. In addition to providing dose-intensity metrics and histograms that can be easily extracted from a plan database and correlated with outcomes, the system can also be extended to a plug-in optimization system, which can directly use the computed metrics for optimization of post-treatment tumor or normal tissue response models. Supported by NIH - P01 - CA059827.« less

Conducting HIV Interventions for Asian Pacific Islander Men Who Have Sex with Men: Challenges and Compromises in Community Collaborative Research

ERIC Educational Resources Information Center

Operario, Don; Nemoto, Tooru; Ng, Terence; Syed, Javid; Mazarei, Mazdak

2005-01-01

This article describes the process of implementing a community collaborative HIV prevention intervention research project targeting Asian and Pacific Islander (API) men who have sex with men (MSM). This article traces the genesis of the project--which linked university researchers with an API-focused community based organization--starting from its…

Coformer screening using thermal analysis based on binary phase diagrams.

PubMed

Yamashita, Hiroyuki; Hirakura, Yutaka; Yuda, Masamichi; Terada, Katsuhide

2014-08-01

The advent of cocrystals has demonstrated a growing need for efficient and comprehensive coformer screening in search of better development forms, including salt forms. Here, we investigated a coformer screening system for salts and cocrystals based on binary phase diagrams using thermal analysis and examined the effectiveness of the method. Indomethacin and tenoxicam were used as models of active pharmaceutical ingredients (APIs). Physical mixtures of an API and 42 kinds of coformers were analyzed using Differential Scanning Calorimetry (DSC) and X-ray DSC. We also conducted coformer screening using a conventional slurry method and compared these results with those from the thermal analysis method and previous studies. Compared with the slurry method, the thermal analysis method was a high-performance screening system, particularly for APIs with low solubility and/or propensity to form solvates. However, this method faced hurdles for screening coformers combined with an API in the presence of kinetic hindrance for salt or cocrystal formation during heating or if there is degradation near the metastable eutectic temperature. The thermal analysis and slurry methods are considered complementary to each other for coformer screening. Feasibility of the thermal analysis method in drug discovery practice is ensured given its small scale and high throughput.

In-line Raman spectroscopic monitoring and feedback control of a continuous twin-screw pharmaceutical powder blending and tableting process.

PubMed

Nagy, Brigitta; Farkas, Attila; Gyürkés, Martin; Komaromy-Hiller, Szofia; Démuth, Balázs; Szabó, Bence; Nusser, Dávid; Borbás, Enikő; Marosi, György; Nagy, Zsombor Kristóf

2017-09-15

The integration of Process Analytical Technology (PAT) initiative into the continuous production of pharmaceuticals is indispensable for reliable production. The present paper reports the implementation of in-line Raman spectroscopy in a continuous blending and tableting process of a three-component model pharmaceutical system, containing caffeine as model active pharmaceutical ingredient (API), glucose as model excipient and magnesium stearate as lubricant. The real-time analysis of API content, blend homogeneity, and tablet content uniformity was performed using a Partial Least Squares (PLS) quantitative method. The in-line Raman spectroscopic monitoring showed that the continuous blender was capable of producing blends with high homogeneity, and technological malfunctions can be detected by the proposed PAT method. The Raman spectroscopy-based feedback control of the API feeder was also established, creating a 'Process Analytically Controlled Technology' (PACT), which guarantees the required API content in the produced blend. This is, to the best of the authors' knowledge, the first ever application of Raman-spectroscopy in continuous blending and the first Raman-based feedback control in the formulation technology of solid pharmaceuticals. Copyright © 2017 Elsevier B.V. All rights reserved.

Software Applications to Access Earth Science Data: Building an ECHO Client

NASA Astrophysics Data System (ADS)

Cohen, A.; Cechini, M.; Pilone, D.

2010-12-01

Historically, developing an ECHO (NASA’s Earth Observing System (EOS) ClearingHOuse) client required interaction with its SOAP API. SOAP, as a framework for web service communication has numerous advantages for Enterprise applications and Java/C# type programming languages. However, as interest has grown for quick development cycles and more intriguing “mashups,” ECHO has seen the SOAP API lose its appeal. In order to address these changing needs, ECHO has introduced two new interfaces facilitating simple access to its metadata holdings. The first interface is built upon the OpenSearch format and ESIP Federated Search framework. The second interface is built upon the Representational State Transfer (REST) architecture. Using the REST and OpenSearch APIs to access ECHO makes development with modern languages much more feasible and simpler. Client developers can leverage the simple interaction with ECHO to focus more of their time on the advanced functionality they are presenting to users. To demonstrate the simplicity of developing with the REST API, participants will be led through a hands-on experience where they will develop an ECHO client that performs the following actions: + Login + Provider discovery + Provider based dataset discovery + Dataset, Temporal, and Spatial constraint based Granule discovery + Online Data Access

Ground System Architectures Workshop GMSEC SERVICES SUITE (GSS): an Agile Development Story

NASA Technical Reports Server (NTRS)

Ly, Vuong

2017-01-01

The GMSEC (Goddard Mission Services Evolution Center) Services Suite (GSS) is a collection of tools and software services along with a robust customizable web-based portal that enables the user to capture, monitor, report, and analyze system-wide GMSEC data. Given our plug-and-play architecture and the needs for rapid system development, we opted to follow the Scrum Agile Methodology for software development. Being one of the first few projects to implement the Agile methodology at NASA GSFC, in this presentation we will present our approaches, tools, successes, and challenges in implementing this methodology. The GMSEC architecture provides a scalable, extensible ground and flight system for existing and future missions. GMSEC comes with a robust Application Programming Interface (GMSEC API) and a core set of Java-based GMSEC components that facilitate the development of a GMSEC-based ground system. Over the past few years, we have seen an upbeat in the number of customers who are moving from a native desktop application environment to a web based environment particularly for data monitoring and analysis. We also see a need to provide separation of the business logic from the GUI display for our Java-based components and also to consolidate all the GUI displays into one interface. This combination of separation and consolidation brings immediate value to a GMSEC-based ground system through increased ease of data access via a uniform interface, built-in security measures, centralized configuration management, and ease of feature extensibility.

HTTP-based Search and Ordering Using ECHO's REST-based and OpenSearch APIs

NASA Astrophysics Data System (ADS)

Baynes, K.; Newman, D. J.; Pilone, D.

2012-12-01

Metadata is an important entity in the process of cataloging, discovering, and describing Earth science data. NASA's Earth Observing System (EOS) ClearingHOuse (ECHO) acts as the core metadata repository for EOSDIS data centers, providing a centralized mechanism for metadata and data discovery and retrieval. By supporting both the ESIP's Federated Search API and its own search and ordering interfaces, ECHO provides multiple capabilities that facilitate ease of discovery and access to its ever-increasing holdings. Users are able to search and export metadata in a variety of formats including ISO 19115, json, and ECHO10. This presentation aims to inform technically savvy clients interested in automating search and ordering of ECHO's metadata catalog. The audience will be introduced to practical and applicable examples of end-to-end workflows that demonstrate finding, sub-setting and ordering data that is bound by keyword, temporal and spatial constraints. Interaction with the ESIP OpenSearch Interface will be highlighted, as will ECHO's own REST-based API.

MARs Tools for Interactive ANalysis (MARTIAN): Google Maps Tools for Visual Exploration of Geophysical Modeling on Mars

NASA Astrophysics Data System (ADS)

Dimitrova, L. L.; Haines, M.; Holt, W. E.; Schultz, R. A.; Richard, G.; Haines, A. J.

2006-12-01

Interactive maps of surface-breaking faults and stress models on Mars provide important tools to engage undergraduate students, educators, and scientists with current geological and geophysical research. We have developed a map based on the Google Maps API -- an Internet based tool combining DHTML and AJAX, -- which allows very large maps to be viewed over the World Wide Web. Typically, small portions of the maps are downloaded as needed, rather than the entire image at once. This set-up enables relatively fast access for users with low bandwidth. Furthermore, Google Maps provides an extensible interactive interface making it ideal for visualizing multiple data sets at the user's choice. The Google Maps API works primarily with data referenced to latitudes and longitudes, which is then mapped in Mercator projection only. We have developed utilities for general cylindrical coordinate systems by converting these coordinates into equivalent Mercator projection before including them on the map. The MARTIAN project is available at http://rock.geo.sunysb.edu/~holt/Mars/MARTIAN/. We begin with an introduction to the Martian surface using a topography model. Faults from several datasets are classified by type (extension vs. compression) and by time epoch. Deviatoric stresses due to gravitational potential energy differences, calculated from the topography and crustal thickness, can be overlain. Several quantitative measures for the fit of the stress field to the faults are also included. We provide introductory text and exercises spanning a range of topics: how are faults identified, what stress is and how it relates to faults, what gravitational potential energy is and how variations in it produce stress, how the models are created, and how these models can be evaluated and interpreted. The MARTIAN tool is used at Stony Brook University in GEO 310: Introduction to Geophysics, a class geared towards junior and senior geosciences majors. Although this project is in its early stages, high school and college teachers, as well as researchers have expressed interest in using and extending these tools for visualizing and interacting with data on Earth and other planetary bodies.

The E3 ubiquitin ligases β-TrCP and FBXW7 cooperatively mediates GSK3-dependent Mcl-1 degradation induced by the Akt inhibitor API-1, resulting in apoptosis.

PubMed

Ren, Hui; Koo, Junghui; Guan, Baoxiang; Yue, Ping; Deng, Xingming; Chen, Mingwei; Khuri, Fadlo R; Sun, Shi-Yong

2013-11-22

The novel Akt inhibitor, API-1, induces apoptosis through undefined mechanisms. The current study focuses on revealing the mechanisms by which API-1 induces apoptosis. API-1 rapidly and potently reduced the levels of Mcl-1 primarily in API-1-senstive lung cancer cell lines. Ectopic expression of Mcl-1 protected cells from induction of apoptosis by API-1. API-1 treatment decreased the half-life of Mcl-1, whereas inhibition of the proteasome with MG132 rescued Mcl-1 reduction induced by API-1. API-1 decreased Mcl-1 levels accompanied with a rapid increase in Mcl-1 phosphorylation (S159/T163). Moreover, inhibition of GSK3 inhibited Mcl-1 phosphorylation and reduction induced by API-1 and antagonized the effect of API-1 on induction of apoptosis. Knockdown of either FBXW7 or β-TrCP alone, both of which are E3 ubiquitin ligases involved in Mcl-1 degradation, only partially rescued Mcl-1 reduction induced by API-1. However, double knockdown of both E3 ubiquitin ligases enhanced the rescue of API-1-induced Mcl-1 reduction. API-1 induces GSK3-dependent, β-TrCP- and FBXW7-mediated Mcl-1 degradation, resulting in induction of apoptosis.

The E3 ubiquitin ligases β-TrCP and FBXW7 cooperatively mediates GSK3-dependent Mcl-1 degradation induced by the Akt inhibitor API-1, resulting in apoptosis

PubMed Central

2013-01-01

Background The novel Akt inhibitor, API-1, induces apoptosis through undefined mechanisms. The current study focuses on revealing the mechanisms by which API-1 induces apoptosis. Results API-1 rapidly and potently reduced the levels of Mcl-1 primarily in API-1-senstive lung cancer cell lines. Ectopic expression of Mcl-1 protected cells from induction of apoptosis by API-1. API-1 treatment decreased the half-life of Mcl-1, whereas inhibition of the proteasome with MG132 rescued Mcl-1 reduction induced by API-1. API-1 decreased Mcl-1 levels accompanied with a rapid increase in Mcl-1 phosphorylation (S159/T163). Moreover, inhibition of GSK3 inhibited Mcl-1 phosphorylation and reduction induced by API-1 and antagonized the effect of API-1 on induction of apoptosis. Knockdown of either FBXW7 or β-TrCP alone, both of which are E3 ubiquitin ligases involved in Mcl-1 degradation, only partially rescued Mcl-1 reduction induced by API-1. However, double knockdown of both E3 ubiquitin ligases enhanced the rescue of API-1-induced Mcl-1 reduction. Conclusions API-1 induces GSK3-dependent, β-TrCP- and FBXW7-mediated Mcl-1 degradation, resulting in induction of apoptosis. PMID:24261825

The Earth Observatory Natural Event Tracker (EONET): An API for Matching Natural Events to GIBS Imagery

NASA Astrophysics Data System (ADS)

Ward, K.

2015-12-01

Hidden within the terabytes of imagery in NASA's Global Imagery Browse Services (GIBS) collection are hundreds of daily natural events. Some events are newsworthy, devastating, and visibly obvious at a global scale, others are merely regional curiosities. Regardless of the scope and significance of any one event, it is likely that multiple GIBS layers can be viewed to provide a multispectral, dataset-based view of the event. To facilitate linking between the discrete event and the representative dataset imagery, NASA's Earth Observatory Group has developed a prototype application programming interface (API): the Earth Observatory Natural Event Tracker (EONET). EONET supports an API model that allows users to retrieve event-specific metadata--date/time, location, and type (wildfire, storm, etc.)--and web service layer-specific metadata which can be used to link to event-relevant dataset imagery in GIBS. GIBS' ability to ingest many near real time datasets, combined with its growing archive of past imagery, means that API users will be able to develop client applications that not only show ongoing events but can also look at imagery from before and after. In our poster, we will present the API and show examples of its use.

Identifying and assessing highly hazardous drugs within quality risk management programs.

PubMed

Sussman, Robert G; Schatz, Anthony R; Kimmel, Tracy A; Ader, Allan; Naumann, Bruce D; Weideman, Patricia A

2016-08-01

Historically, pharmaceutical industry regulatory guidelines have assigned certain active pharmaceutical ingredients (APIs) to various categories of concern, such as "cytotoxic", "hormones", and "steroids". These categories have been used to identify APIs requiring segregation or dedication in order to prevent cross-contamination and protect the quality and safety of drug products. Since these terms were never defined by regulatory authorities, and many novel pharmacological mechanisms challenge these categories, there is a recognized need to modify the historical use of these terms. The application of a risk-based approach using a health-based limit, such as an acceptable daily exposure (ADE), is more appropriate for the development of a Quality Risk Management Program (QRMP) than the use of categories of concern. The toxicological and pharmacological characteristics of these categories are discussed to help identify and prioritize compounds requiring special attention. Controlling airborne concentrations and the contamination of product contact surfaces in accordance with values derived from quantitative risk assessments can prevent adverse effects in workers and patients, regardless of specific categorical designations to which these APIs have been assigned. The authors acknowledge the movement away from placing compounds into categories and, while not yet universal, the importance of basing QRMPs on compound-specific ADEs and risk assessments. Based on the results of a risk assessment, segregation and dedication may also be required for some compounds to prevent cross contamination during manufacture of APIs. Copyright © 2016 Elsevier Inc. All rights reserved.

Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

PubMed Central

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-01-01

Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact: peter@biomatters.com PMID:22543367

Geneious Basic: an integrated and extendable desktop software platform for the organization and analysis of sequence data.

PubMed

Kearse, Matthew; Moir, Richard; Wilson, Amy; Stones-Havas, Steven; Cheung, Matthew; Sturrock, Shane; Buxton, Simon; Cooper, Alex; Markowitz, Sidney; Duran, Chris; Thierer, Tobias; Ashton, Bruce; Meintjes, Peter; Drummond, Alexei

2012-06-15

The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl.

Similar Comparative Low and High Doses of Deltamethrin and Acetamiprid Differently Impair the Retrieval of the Proboscis Extension Reflex in the Forager Honey Bee (Apis mellifera).

PubMed

Thany, Steeve H; Bourdin, Céline M; Graton, Jérôme; Laurent, Adèle D; Mathé-Allainmat, Monique; Lebreton, Jacques; Questel, Jean-Yves le

2015-09-28

In the present study, the effects of low (10 ng/bee) and high (100 ng/bee) doses of acetamiprid and deltamethrin insecticides on multi-trial learning and retrieval were evaluated in the honey bee Apis mellifera. After oral application, acetamiprid and deltamethrin at the concentrations used were not able to impair learning sessions. When the retention tests were performed 1 h, 6 h, and 24 h after learning, we found a significant difference between bees after learning sessions when drugs were applied 24 h before learning. Deltamethrin-treated bees were found to be more sensitive at 10 ng/bee and 100 ng/bee doses compared to acetamiprid-treated bees, only with amounts of 100 ng/bee and at 6 h and 24 h delays. When insecticides were applied during learning sessions, none of the tested insecticides was able to impair learning performance at 10 ng/bee or 100 ng/bee but retention performance was altered 24 h after learning sessions. Acetamiprid was the only one to impair retrieval at 10 ng/bee, whereas at 100 ng/bee an impairment of retrieval was found with both insecticides. The present results therefore suggest that acetamiprid and deltamethrin are able to impair retrieval performance in the honey bee Apis mellifera.

APIS-a novel approach for conditioning honey bees.

PubMed

Kirkerud, Nicholas H; Wehmann, Henja-Niniane; Galizia, C Giovanni; Gustav, David

2013-01-01

Honey bees perform robustly in different conditioning paradigms. This makes them excellent candidates for studying mechanisms of learning and memory at both an individual and a population level. Here we introduce a novel method of honey bee conditioning: APIS, the Automatic Performance Index System. In an enclosed walking arena where the interior is covered with an electric grid, presentation of odors from either end can be combined with weak electric shocks to form aversive associations. To quantify behavioral responses, we continuously monitor the movement of the bee by an automatic tracking system. We found that escapes from one side to the other, changes in velocity as well as distance and time spent away from the punished odor are suitable parameters to describe the bee's learning capabilities. Our data show that in a short-term memory test the response rate for the conditioned stimulus (CS) in APIS correlates well with response rate obtained from conventional Proboscis Extension Response (PER)-conditioning. Additionally, we discovered that bees modulate their behavior to aversively learned odors by reducing their rate, speed and magnitude of escapes and that both generalization and extinction seem to be different between appetitive and aversive stimuli. The advantages of this automatic system make it ideal for assessing learning rates in a standardized and convenient way, and its flexibility adds to the toolbox for studying honey bee behavior.

DyninstAPI Patches

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

LeGendre, M.

2012-04-01

We are seeking a code review of patches against DyninstAPI 8.0. DyninstAPI is an open source binary instrumentation library from the University of Wisconsin and University of Maryland. Our patches port DyninstAPI to the BlueGene/P and BlueGene/Q systems, as well as fix DyninstAPI bugs and implement minor new features in DyninstAPI.

Modeling and Simulation Behavior Validation Methodology and Extension Model Validation for the Individual Soldier

DTIC Science & Technology

2015-03-01

domains. Major model functions include: • Ground combat: Light and heavy forces. • Air mobile forces. • Future forces. • Fixed-wing and rotary-wing...Constraints: • Study must be completed no later than 31 December 2014. • Entity behavior limited to select COMBATXXI Mobility , Unmanned Aerial System...and SQL backend , as well as any open application programming interface API. • Allows data transparency and data driven navigation through the model

Reuse of the Cloud Analytics and Collaboration Environment within Tactical Applications (TacApps): A Feasibility Analysis

DTIC Science & Technology

2016-03-01

Representational state transfer  Java messaging service  Java application programming interface (API)  Internet relay chat (IRC)/extensible messaging and...JBoss application server or an Apache Tomcat servlet container instance. The relational database management system can be either PostgreSQL or MySQL ... Java library called direct web remoting. This library has been part of the core CACE architecture for quite some time; however, there have not been

High-throughput molecular identification of Staphylococcus spp. isolated from a clean room facility in an environmental monitoring program

PubMed Central

2010-01-01

Background The staphylococci are one of the most common environmental isolates found in clean room facility. Consequently, isolation followed by comprehensive and accurate identification is an essential step in any environmental monitoring program. Findings We have used the API Staph identification kit (bioMérieux, France) which depends on the expression of metabolic activities and or morphological features to identify the Staphylococcus isolates. The API staphylococci showed low sensitivity in the identification of some species, so we performed molecular methods based on PCR based fingerprinting of glyceraldehyde-3-phosphate dehydrogenase encoding gene as useful taxonomic tool for examining Staphylococcus isolates. Conclusions Our results showed that PCR protocol used in this study which depends on genotypic features was relatively accurate, rapid, sensitive and superior in the identification of at least 7 species of Staphylococcus than API Staph which depends on phenotypic features. PMID:21047438

High-throughput molecular identification of Staphylococcus spp. isolated from a clean room facility in an environmental monitoring program.

PubMed

Sheraba, Norhan S; Yassin, Aymen S; Amin, Magdy A

2010-11-04

The staphylococci are one of the most common environmental isolates found in clean room facility. Consequently, isolation followed by comprehensive and accurate identification is an essential step in any environmental monitoring program. We have used the API Staph identification kit (bioMérieux, France) which depends on the expression of metabolic activities and or morphological features to identify the Staphylococcus isolates. The API staphylococci showed low sensitivity in the identification of some species, so we performed molecular methods based on PCR based fingerprinting of glyceraldehyde-3-phosphate dehydrogenase encoding gene as useful taxonomic tool for examining Staphylococcus isolates. Our results showed that PCR protocol used in this study which depends on genotypic features was relatively accurate, rapid, sensitive and superior in the identification of at least 7 species of Staphylococcus than API Staph which depends on phenotypic features.

Improved recombinant Api m 1- and Ves v 5-based IgE testing to dissect bee and yellow jacket allergy and their correlation with the severity of the sting reaction.

PubMed

Šelb, J; Kogovšek, R; Šilar, M; Košnik, M; Korošec, P

2016-04-01

No study has assessed the diagnostic sensitivity of rApi m 1 and rVes v 5 on Immulite testing system. To compare the diagnostic sensitivity of commercially available venom recombinant allergens between the currently available immunoassays [ImmunoCAP (CAP) and Immulite (LITE)] and establish their correlation with the severity of the sting reaction. This study evaluated 95 bee venom and 110 yellow jacket venom-allergic subjects. We measured the levels of sIgE to rApi m 1, rVes v 5 (LITE and CAP), rApi m 2 (LITE), rVes v 1 (CAP) and total IgE (CAP). Forty-nine healthy subjects served as controls. The diagnostic sensitivity of rApi m 1 and rVes v 5 was significantly higher with the LITE than with the CAP system (71% vs. 88% and 82% vs. 93%). The specificity of both assays for both allergens was between 94% and 98%. Twenty-nine patients that tested negative for rApi m 1 or rVes v 5 with CAP were positive with LITE, but none of the patients that tested negative with LITE were positive with CAP. The positive values of rApi m 1 and rVes v 5 were on average 2.7 and 2.3 times higher, with the LITE than with the CAP system. The combination of rApi m 1 and rApi m 2 (LITE) and the combination of rVes v 5 (LITE) and rVes v 1 (CAP) almost matched the sensitivity of native venoms (95% and 97%, respectively), whereas the diagnostic sensitivity of the combination of rVes v 5 and rVes v 1 (CAP) did not reach the sensitivity of rVes v 5 (LITE) alone (90% vs. 93%). IgE levels to venom recombinants and total IgE did not correlate with the severity of sting reaction. The use of rApi m 1 and rVes v 5 with the LITE system significantly enhanced diagnostic utility of venom recombinants and should improve the dissection of bee and yellow jacket venom allergy. © 2015 John Wiley & Sons Ltd.

Fusion of the C-terminal triskaidecapeptide of hirudin variant 3 to alpha1-proteinase inhibitor M358R increases the serpin-mediated rate of thrombin inhibition

PubMed Central

2013-01-01

Background Alpha-1 proteinase inhibitor (API) is a plasma serpin superfamily member that inhibits neutrophil elastase; variant API M358R inhibits thrombin and activated protein C (APC). Fusing residues 1-75 of another serpin, heparin cofactor II (HCII), to API M358R (in HAPI M358R) was previously shown to accelerate thrombin inhibition over API M358R by conferring thrombin exosite 1 binding properties. We hypothesized that replacing HCII 1-75 region with the 13 C-terminal residues (triskaidecapeptide) of hirudin variant 3 (HV354-66) would further enhance the inhibitory potency of API M358R fusion proteins. We therefore expressed HV3API M358R (HV354-66 fused to API M358R) and HV3API RCL5 (HV354-66 fused to API F352A/L353V/E354V/A355I/I356A/I460L/M358R) API M358R) as N-terminally hexahistidine-tagged polypeptides in E. coli. Results HV3API M358R inhibited thrombin 3.3-fold more rapidly than API M358R; for HV3API RCL5 the rate enhancement was 1.9-fold versus API RCL5; neither protein inhibited thrombin as rapidly as HAPI M358R. While the thrombin/Activated Protein C rate constant ratio was 77-fold higher for HV3API RCL5 than for HV3API M358R, most of the increased specificity derived from the API F352A/L353V/E354V/A355I/I356A/I460L API RCL 5 mutations, since API RCL5 remained 3-fold more specific than HV3API RCL5. An HV3 54-66 peptide doubled the Thrombin Clotting Time (TCT) and halved the binding of thrombin to immobilized HCII 1-75 at lower concentrations than free HCII 1-75. HV3API RCL5 bound active site-inhibited FPR-chloromethyl ketone-thrombin more effectively than HAPI RCL5. Transferring the position of the fused HV3 triskaidecapeptide to the C-terminus of API M358R decreased the rate of thrombin inhibition relative to that mediated by HV3API M358R by 11-to 14-fold. Conclusions Fusing the C-terminal triskaidecapeptide of HV3 to API M358R-containing serpins significantly increased their effectiveness as thrombin inhibitors, but the enhancement was less than that seen in HCII 1-75–API M358R fusion proteins. HCII 1-75 was a superior fusion partner, in spite of the greater affinity of the HV3 triskaidecapeptide, manifested both in isolated and API-fused form, for thrombin exosite 1. Our results suggest that HCII 1-75 binds thrombin exosite 1 and orients the attached serpin scaffold for more efficient interaction with the active site of thrombin than the HV3 triskaidecapeptide. PMID:24215622

Kiwifruit Flower Odor Perception and Recognition by Honey Bees, Apis mellifera.

PubMed

Twidle, Andrew M; Mas, Flore; Harper, Aimee R; Horner, Rachael M; Welsh, Taylor J; Suckling, David M

2015-06-17

Volatile organic compounds (VOCs) from male and female kiwifruit (Actinidia deliciosa 'Hayward') flowers were collected by dynamic headspace sampling. Honey bee (Apis mellifera) perception of the flower VOCs was tested using gas chromatography coupled to electroantennogram detection. Honey bees consistently responded to six compounds present in the headspace of female kiwifruit flowers and five compounds in the headspace of male flowers. Analysis of the floral volatiles by gas chromatography-mass spectrometry and microscale chemical derivatization showed the compounds to be nonanal, 2-phenylethanol, 4-oxoisophorone, (3E,6E)-α-farnesene, (6Z,9Z)-heptadecadiene, and (8Z)-heptadecene. Bees were then trained via olfactory conditioning of the proboscis extension response (PER) to synthetic mixtures of these compounds using the ratios present in each flower type. Honey bees trained to the synthetic mixtures showed a high response to the natural floral extracts, indicating that these may be the key compounds for honey bee perception of kiwifruit flower odor.

A Data Services Upgrade for Advanced Composition Explorer (ACE) Data

NASA Astrophysics Data System (ADS)

Davis, A. J.; Hamell, G.

2008-12-01

Since early in 1998, NASA's Advanced Composition Explorer (ACE) spacecraft has provided continuous measurements of solar wind, interplanetary magnetic field, and energetic particle activity from L1, located approximately 0.01 AU sunward of Earth. The spacecraft has enough fuel to stay in orbit about L1 until ~2024. The ACE Science Center (ASC) provides access to ACE data, and performs level 1 and browse data processing for the science instruments. Thanks to a NASA Data Services Upgrade grant, we have recently retooled our legacy web interface to ACE data, enhancing data subsetting capabilities and improving online plotting options. We have also integrated a new application programming interface (API) and we are working to ensure that it will be compatible with emerging Virtual Observatory (VO) data services standards. The new API makes extensive use of metadata created using the Space Physics Archive Search and Extract (SPASE) data model. We describe these recent improvements to the ACE Science Center data services, and our plans for integrating these services into the VO system.

Nosema ceranae in South American Native Stingless Bees and Social Wasp.

PubMed

Porrini, Martín Pablo; Porrini, Leonardo Pablo; Garrido, Paula Melisa; de Melo E Silva Neto, Carlos; Porrini, Darío Pablo; Muller, Fernando; Nuñez, Laura Alejandra; Alvarez, Leopoldo; Iriarte, Pedro Fernandez; Eguaras, Martín Javier

2017-11-01

Besides the incipient research effort, the role of parasites as drivers of the reduction affecting pollinator populations is mostly unknown. Given the worldwide extension of the beekeeping practice and the diversity of pathogens affecting Apis mellifera populations, honey bee colonies are a certain source of parasite dispersion to other species. Here, we communicate the detection of the microsporidium Nosema ceranae, a relatively new parasite of honey bees, in stingless bees (Meliponini) and the social wasp Polybia scutellaris (Vespidae) samples from Argentina and Brazil by means of duplex PCR. Beyond the geographic location of the nests, N. ceranae was detected in seven from the eight Meliponini species analyzed, while Nosema apis, another common parasite of A. mellifera, was absent in all samples tested. Further research is necessary to determine if the presence of the parasite is also associated with established infection in host tissues. The obtained information enriches the current knowledge about pathologies that can infect or, at least, be vectored by native wild pollinators from South America.

First detection of the larval chalkbrood disease pathogen Ascosphaera apis (Ascomycota: Eurotiomycetes: Ascosphaerales) in adult bumble bees.

PubMed

Maxfield-Taylor, Sarah A; Mujic, Alija B; Rao, Sujaya

2015-01-01

Fungi in the genus Ascosphaera (Ascomycota: Eurotiomycetes: Ascosphaerales) cause chalkbrood disease in larvae of bees. Here, we report the first-ever detection of the fungus in adult bumble bees that were raised in captivity for studies on colony development. Wild queens of Bombus griseocollis, B. nevadensis and B. vosnesenskii were collected and maintained for establishment of nests. Queens that died during rearing or that did not lay eggs within one month of capture were dissected, and tissues were examined microscopically for the presence of pathogens. Filamentous fungi that were detected were plated on artificial media containing broad spectrum antibiotics for isolation and identification. Based on morphological characters, the fungus was identified as Ascosphaera apis (Maasen ex Claussen) Olive and Spiltoir, a species that has been reported earlier only from larvae of the European honey bee, Apis mellifera, the Asian honey bee, Apis cerana, and the carpenter bee Xylocopa californica arizonensis. The identity of the fungus was confirmed using molecular markers and phylogenetic analysis. Ascosphaera apis was detected in queens of all three bumble bee species examined. Of 150 queens dissected, 12 (8%) contained vegetative and reproductive stages of the fungus. Both fungal stages were also detected in two workers collected from colonies with Ascosphaera-infected B. nevadensis queens. In this study, wild bees could have been infected prior to capture for rearing, or, the A. apis infection could have originated via contaminated European honey bee pollen fed to the bumble bees in captivity. Thus, the discovery of A. apis in adult bumble bees in the current study has important implications for commercial production of bumble bee colonies and highlights potential risks to native bees via pathogen spillover from infected bees and infected pollen.

Transcriptome analysis of the honey bee fungal pathogen, Ascosphaera apis: implications for host pathogenesis

PubMed Central

2012-01-01

Background We present a comprehensive transcriptome analysis of the fungus Ascosphaera apis, an economically important pathogen of the Western honey bee (Apis mellifera) that causes chalkbrood disease. Our goals were to further annotate the A. apis reference genome and to identify genes that are candidates for being differentially expressed during host infection versus axenic culture. Results We compared A. apis transcriptome sequence from mycelia grown on liquid or solid media with that dissected from host-infected tissue. 454 pyrosequencing provided 252 Mb of filtered sequence reads from both culture types that were assembled into 10,087 contigs. Transcript contigs, protein sequences from multiple fungal species, and ab initio gene predictions were included as evidence sources in the Maker gene prediction pipeline, resulting in 6,992 consensus gene models. A phylogeny based on 12 of these protein-coding loci further supported the taxonomic placement of Ascosphaera as sister to the core Onygenales. Several common protein domains were less abundant in A. apis compared with related ascomycete genomes, particularly cytochrome p450 and protein kinase domains. A novel gene family was identified that has expanded in some ascomycete lineages, but not others. We manually annotated genes with homologs in other fungal genomes that have known relevance to fungal virulence and life history. Functional categories of interest included genes involved in mating-type specification, intracellular signal transduction, and stress response. Computational and manual annotations have been made publicly available on the Bee Pests and Pathogens website. Conclusions This comprehensive transcriptome analysis substantially enhances our understanding of the A. apis genome and its expression during infection of honey bee larvae. It also provides resources for future molecular studies of chalkbrood disease and ultimately improved disease management. PMID:22747707

libRoadRunner: a high performance SBML simulation and analysis library

PubMed Central

Somogyi, Endre T.; Bouteiller, Jean-Marie; Glazier, James A.; König, Matthias; Medley, J. Kyle; Swat, Maciej H.; Sauro, Herbert M.

2015-01-01

Motivation: This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations. Results: libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB (www.mathworks.com) and SciPy (http://www.scipy.org/), making it fast and easy to learn. libRoadRunner uses a custom Just-In-Time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix. Availability and implementation: libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository. Contacts: hsauro@u.washington.edu or somogyie@indiana.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26085503

libRoadRunner: a high performance SBML simulation and analysis library.

PubMed

Somogyi, Endre T; Bouteiller, Jean-Marie; Glazier, James A; König, Matthias; Medley, J Kyle; Swat, Maciej H; Sauro, Herbert M

2015-10-15

This article presents libRoadRunner, an extensible, high-performance, cross-platform, open-source software library for the simulation and analysis of models expressed using Systems Biology Markup Language (SBML). SBML is the most widely used standard for representing dynamic networks, especially biochemical networks. libRoadRunner is fast enough to support large-scale problems such as tissue models, studies that require large numbers of repeated runs and interactive simulations. libRoadRunner is a self-contained library, able to run both as a component inside other tools via its C++ and C bindings, and interactively through its Python interface. Its Python Application Programming Interface (API) is similar to the APIs of MATLAB ( WWWMATHWORKSCOM: ) and SciPy ( HTTP//WWWSCIPYORG/: ), making it fast and easy to learn. libRoadRunner uses a custom Just-In-Time (JIT) compiler built on the widely used LLVM JIT compiler framework. It compiles SBML-specified models directly into native machine code for a variety of processors, making it appropriate for solving extremely large models or repeated runs. libRoadRunner is flexible, supporting the bulk of the SBML specification (except for delay and non-linear algebraic equations) including several SBML extensions (composition and distributions). It offers multiple deterministic and stochastic integrators, as well as tools for steady-state analysis, stability analysis and structural analysis of the stoichiometric matrix. libRoadRunner binary distributions are available for Mac OS X, Linux and Windows. The library is licensed under Apache License Version 2.0. libRoadRunner is also available for ARM-based computers such as the Raspberry Pi. http://www.libroadrunner.org provides online documentation, full build instructions, binaries and a git source repository. hsauro@u.washington.edu or somogyie@indiana.edu Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

N-Terminal Ile-Orn- and Trp-Orn-Motif Repeats Enhance Membrane Interaction and Increase the Antimicrobial Activity of Apidaecins against Pseudomonas aeruginosa

PubMed Central

Bluhm, Martina E. C.; Schneider, Viktoria A. F.; Schäfer, Ingo; Piantavigna, Stefania; Goldbach, Tina; Knappe, Daniel; Seibel, Peter; Martin, Lisandra L.; Veldhuizen, Edwin J. A.; Hoffmann, Ralf

2016-01-01

The Gram-negative bacterium Pseudomonas aeruginosa is a life-threatening nosocomial pathogen due to its generally low susceptibility toward antibiotics. Furthermore, many strains have acquired resistance mechanisms requiring new antimicrobials with novel mechanisms to enhance treatment options. Proline-rich antimicrobial peptides, such as the apidaecin analog Api137, are highly efficient against various Enterobacteriaceae infections in mice, but less active against P. aeruginosa in vitro. Here, we extended our recent work by optimizing lead peptides Api755 (gu-OIORPVYOPRPRPPHPRL-OH; gu = N,N,N′,N′-tetramethylguanidino, O = L-ornithine) and Api760 (gu-OWORPVYOPRPRPPHPRL-OH) by incorporation of Ile-Orn- and Trp-Orn-motifs, respectively. Api795 (gu-O(IO)2RPVYOPRPRPPHPRL-OH) and Api794 (gu-O(WO)3RPVYOPRPRPPHPRL-OH) were highly active against P. aeruginosa with minimal inhibitory concentrations of 8–16 and 8–32 μg/mL against Escherichia coli and Klebsiella pneumoniae. Assessed using a quartz crystal microbalance, these peptides inserted into a membrane layer and the surface activity increased gradually from Api137, over Api795, to Api794. This mode of action was confirmed by transmission electron microscopy indicating some membrane damage only at the high peptide concentrations. Api794 and Api795 were highly stable against serum proteases (half-life times >5 h) and non-hemolytic to human erythrocytes at peptide concentrations of 0.6 g/L. At this concentration, Api795 reduced the cell viability of HeLa cells only slightly, whereas the IC50 of Api794 was 0.23 ± 0.09 g/L. Confocal fluorescence microscopy revealed no colocalization of 5(6)-carboxyfluorescein-labeled Api794 or Api795 with the mitochondria, excluding interactions with the mitochondrial membrane. Interestingly, Api795 was localized in endosomes, whereas Api794 was present in endosomes and the cytosol. This was verified using flow cytometry showing a 50% higher uptake of Api794 in HeLa cells compared with Api795. The uptake was reduced for both peptides by 50 and 80%, respectively, after inhibiting endocytotic uptake with dynasore. In summary, Api794 and Api795 were highly active against P. aeruginosa in vitro. Both peptides passed across the bacterial membrane efficiently, most likely then disturbing the ribosome assembly, and resulting in further intracellular damage. Api795 with its IOIO-motif, which was particularly active and only slightly toxic in vitro, appears to represent a promising third generation lead compound for the development of novel antibiotics against P. aeruginosa. PMID:27243004

CALIBRATION, OPTIMIZATION, AND SENSITIVITY AND UNCERTAINTY ALGORITHMS APPLICATION PROGRAMMING INTERFACE (COSU-API)

EPA Science Inventory

The Application Programming Interface (API) for Uncertainty Analysis, Sensitivity Analysis, and Parameter Estimation (UA/SA/PE API) tool development, here fore referred to as the Calibration, Optimization, and Sensitivity and Uncertainty Algorithms API (COSU-API), was initially d...

jmzML, an open-source Java API for mzML, the PSI standard for MS data.

PubMed

Côté, Richard G; Reisinger, Florian; Martens, Lennart

2010-04-01

We here present jmzML, a Java API for the Proteomics Standards Initiative mzML data standard. Based on the Java Architecture for XML Binding and XPath-based XML indexer random-access XML parser, jmzML can handle arbitrarily large files in minimal memory, allowing easy and efficient processing of mzML files using the Java programming language. jmzML also automatically resolves internal XML references on-the-fly. The library (which includes a viewer) can be downloaded from http://jmzml.googlecode.com.

Impact of Nosema ceranae and Nosema apis on individual worker bees of the two host species (Apis cerana and Apis mellifera) and regulation of host immune response.

PubMed

Sinpoo, Chainarong; Paxton, Robert J; Disayathanoowat, Terd; Krongdang, Sasiprapa; Chantawannakul, Panuwan

Nosema apis and Nosema ceranae are obligate intracellular microsporidian parasites infecting midgut epithelial cells of host adult honey bees, originally Apis mellifera and Apis cerana respectively. Each microsporidia cross-infects the other host and both microsporidia nowadays have a worldwide distribution. In this study, cross-infection experiments using both N. apis and N. ceranae in both A. mellifera and A. cerana were carried out to compare pathogen proliferation and impact on hosts, including host immune response. Infection by N. ceranae led to higher spore loads than by N. apis in both host species, and there was greater proliferation of microsporidia in A. mellifera compared to A. cerana. Both N. apis and N. ceranae were pathogenic in both host Apis species. N. ceranae induced subtly, though not significantly, higher mortality than N. apis in both host species, yet survival of A. cerana was no different to that of A. mellifera in response to N. apis or N. ceranae. Infections of both host species with N. apis and N. ceranae caused significant up-regulation of AMP genes and cellular mediated immune genes but did not greatly alter apoptosis-related gene expression. In this study, A. cerana enlisted a higher immune response and displayed lower loads of N. apis and N. ceranae spores than A. mellifera, suggesting it may be better able to defend itself against microsporidia infection. We caution against over-interpretation of our results, though, because differences between host and parasite species in survival were insignificant and because size differences between microsporidia species and between host Apis species may alternatively explain the differential proliferation of N. ceranae in A. mellifera. Copyright © 2017 Elsevier Ltd. All rights reserved.

Cocrystal Solubility Product Prediction Using an in combo Model and Simulations to Improve Design of Experiments.

PubMed

Avdeef, Alex

2018-02-02

To predict the aqueous solubility product (K sp ) and the solubility enhancement of cocrystals (CCs), using an approach based on measured drug and coformer intrinsic solubility (S 0 API , S 0 cof ), combined with in silico H-bond descriptors. A regression model was constructed, assuming that the concentration of the uncharged drug (API) can be nearly equated to drug intrinsic solubility (S 0 API ) and that the concentration of the uncharged coformer can be estimated from a linear combination of the log of the coformer intrinsic solubility, S 0 cof , plus in silico H-bond descriptors (Abraham acidities, α, and basicities, β). The optimal model found for n:1 CCs (-log 10 form) is pK sp  = 1.12 n pS 0 API  + 1.07 pS 0 cof  + 1.01 + 0.74 α API ·β cof  - 0.61 β API ; r 2  = 0.95, SD = 0.62, N = 38. In illustrative CC systems with unknown K sp , predicted K sp was used in simulation of speciation-pH profiles. The extent and pH dependence of solubility enhancement due to CC formation were examined. Suggestions to improve assay design were made. The predicted CC K sp can be used to simulate pH-dependent solution characteristics of saturated systems containing CCs, with the aim of ranking the selection of coformers, and of optimizing the design of experiments.

Chronic toxicity of an environmentally relevant mixture of pharmaceuticals to three aquatic organisms (alga, daphnid, and fish).

PubMed

Watanabe, Haruna; Tamura, Ikumi; Abe, Ryoko; Takanobu, Hitomi; Nakamura, Ataru; Suzuki, Toshinari; Hirose, Akihiko; Nishimura, Tetsuji; Tatarazako, Norihisa

2016-04-01

Principles of concentration addition and independent action have been used as effective tools to predict mixture toxicity based on individual component toxicity. The authors investigated the toxicity of a pharmaceutical mixture composed of the top 10 detected active pharmaceutical ingredients (APIs) in the Tama River (Tokyo, Japan) in a relevant concentration ratio. Both individual and mixture toxicities of the 10 APIs were evaluated by 3 short-term chronic toxicity tests using the alga Pseudokirchneriella subcapitata, the daphnid Ceriodaphnia dubia, and the zebrafish Danio rerio. With the exception of clarithromycin toxicity to alga, the no-observed-effect concentration of individual APIs for each test species was dramatically higher than the highest concentration of APIs found in the environment. The mixture of 10 APIs resulted in toxicity to alga, daphnid, and fish at 6.25 times, 100 times, and 15,000 times higher concentrations, respectively, than the environmental concentrations of individual APIs. Predictions by concentration addition and independent action were nearly identical for alga, as clarithromycin was the predominant toxicant in the mixture. Both predictions described the observed mixture toxicity to alga fairly well, whereas they slightly underestimated the observed mixture toxicity in the daphnid test. In the fish embryo test, the observed toxicity fell between the predicted toxicity by concentration addition and independent action. These results suggested that the toxicity of environmentally relevant pharmaceutical mixtures could be predicted by individual toxicity using either concentration addition or independent action. © 2015 SETAC.

Targeted expansion project for outreach and treatment for substance abuse and HIV risk behaviors in Asian and Pacific Islander communities.

PubMed

Nemoto, Tooru; Iwamoto, Mariko; Kamitani, Emiko; Morris, Anne; Sakata, Maria

2011-04-01

Access to culturally competent HIV/AIDS and substance abuse treatment and prevention services is limited for Asian and Pacific Islanders (APIs). Based on the intake data for a community outreach project in the San Francisco Bay Area (N = 1,349), HIV risk behaviors were described among the targeted API risk groups. The self-reported HIV prevalence was 6% among MSM. Inconsistent condom use for vaginal sex with casual partners in the past 6 months was reported among substance users (43%) and incarcerated participants (60%), whereas 26% of men who have sex with men reported inconsistent condom use for anal sex with casual partners. Overall, 56% and 29% had engaged in sex with casual partners under the influence of alcohol and drugs in the past 6 months, respectively. Although API organizations in the Bay Area have spearheaded HIV prevention, future programs must address substance use issues in relation to sexual risk behaviors, specific to API risk groups.

The Vector, Signal, and Image Processing Library (VSIPL): an Open Standard for Astronomical Data Processing

NASA Astrophysics Data System (ADS)

Kepner, J. V.; Janka, R. S.; Lebak, J.; Richards, M. A.

1999-12-01

The Vector/Signal/Image Processing Library (VSIPL) is a DARPA initiated effort made up of industry, government and academic representatives who have defined an industry standard API for vector, signal, and image processing primitives for real-time signal processing on high performance systems. VSIPL supports a wide range of data types (int, float, complex, ...) and layouts (vectors, matrices and tensors) and is ideal for astronomical data processing. The VSIPL API is intended to serve as an open, vendor-neutral, industry standard interface. The object-based VSIPL API abstracts the memory architecture of the underlying machine by using the concept of memory blocks and views. Early experiments with VSIPL code conversions have been carried out by the High Performance Computing Program team at the UCSD. Commercially, several major vendors of signal processors are actively developing implementations. VSIPL has also been explicitly required as part of a recent Rome Labs teraflop procurement. This poster presents the VSIPL API, its functionality and the status of various implementations.

Students academic performance based on behavior

NASA Astrophysics Data System (ADS)

Maulida, Juwita Dien; Kariyam

2017-12-01

Utilization of data in an information system that can be used for decision making that utilizes existing data warehouse to help dig useful information to make decisions correctly and accurately. Experience API (xAPI) is one of the enabling technologies for collecting data, so xAPI can be used as a data warehouse that can be used for various needs. One software application whose data is collected in xAPI is LMS. LMS is a software used in an electronic learning process that can handle all aspects of learning, by using LMS can also be known how the learning process and the aspects that can affect learning achievement. One of the aspects that can affect the learning achievement is the background of each student, which is not necessarily the student with a good background is an outstanding student or vice versa. Therefore, an action is needed to anticipate this problem. Prediction of student academic performance using Naive Bayes algorithm obtained accuracy of 67.7983% and error 32.2917%.

Mechanical Characteristics of Submerged Arc Weldment in API Gas Pipeline Steel of Grade X65

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

Hashemi, S. H.; Mohammadyani, D.

The mechanical properties of submerged arc weldment (SAW) in gas transportation pipeline steel of grade API X65 (65 ksi yield strength) were investigated. This steel is produced by thermo mechanical control rolled (TMC), and is largely used in Iran gas piping systems and networks. The results from laboratory study on three different regions; i.e. base metal (BM), fusion zone (FZ) and heat affected zone (HAZ) were used to compare weldment mechanical characteristics with those specified by API 5L (revision 2004) standard code. Different laboratory experiments were conducted on test specimens taken from 48 inch outside diameter and 14.3 mm wallmore » thickness gas pipeline. The test results showed a gradient of microstructure and Vickers hardness data from the centerline of FZ towards the unaffected MB. Similarly, lower Charpy absorbed energy (compared to BM) was observed in the FZ impact specimens. Despite this, the API specifications were fulfilled in three tested zones, ensuring pipeline structural integrity under working conditions.« less

pysimm: A Python Package for Simulation of Molecular Systems

NASA Astrophysics Data System (ADS)

Fortunato, Michael; Colina, Coray

pysimm, short for python simulation interface for molecular modeling, is a python package designed to facilitate the structure generation and simulation of molecular systems through convenient and programmatic access to object-oriented representations of molecular system data. This poster presents core features of pysimm and design philosophies that highlight a generalized methodology for incorporation of third-party software packages through API interfaces. The integration with the LAMMPS simulation package is explained to demonstrate this methodology. pysimm began as a back-end python library that powered a cloud-based application on nanohub.org for amorphous polymer simulation. The extension from a specific application library to general purpose simulation interface is explained. Additionally, this poster highlights the rapid development of new applications to construct polymer chains capable of controlling chain morphology such as molecular weight distribution and monomer composition.

A Process Analytical Technology (PAT) approach to control a new API manufacturing process: development, validation and implementation.

PubMed

Schaefer, Cédric; Clicq, David; Lecomte, Clémence; Merschaert, Alain; Norrant, Edith; Fotiadu, Frédéric

2014-03-01

Pharmaceutical companies are progressively adopting and introducing Process Analytical Technology (PAT) and Quality-by-Design (QbD) concepts promoted by the regulatory agencies, aiming the building of the quality directly into the product by combining thorough scientific understanding and quality risk management. An analytical method based on near infrared (NIR) spectroscopy was developed as a PAT tool to control on-line an API (active pharmaceutical ingredient) manufacturing crystallization step during which the API and residual solvent contents need to be precisely determined to reach the predefined seeding point. An original methodology based on the QbD principles was designed to conduct the development and validation of the NIR method and to ensure that it is fitted for its intended use. On this basis, Partial least squares (PLS) models were developed and optimized using chemometrics methods. The method was fully validated according to the ICH Q2(R1) guideline and using the accuracy profile approach. The dosing ranges were evaluated to 9.0-12.0% w/w for the API and 0.18-1.50% w/w for the residual methanol. As by nature the variability of the sampling method and the reference method are included in the variability obtained for the NIR method during the validation phase, a real-time process monitoring exercise was performed to prove its fit for purpose. The implementation of this in-process control (IPC) method on the industrial plant from the launch of the new API synthesis process will enable automatic control of the final crystallization step in order to ensure a predefined quality level of the API. In addition, several valuable benefits are expected including reduction of the process time, suppression of a rather difficult sampling and tedious off-line analyses. © 2013 Published by Elsevier B.V.

Targeted Expansion Project for Outreach and Treatment for Substance Abuse and HIV Risk Behaviors in Asian and Pacific Islander Communities

ERIC Educational Resources Information Center

Nemoto, Tooru; Iwamoto, Mariko; Kamitani, Emiko; Morris, Anne; Sakata, Maria

2011-01-01

Access to culturally competent HIV/AIDS and substance abuse treatment and prevention services is limited for Asian and Pacific Islanders (APIs). Based on the intake data for a community outreach project in the San Francisco Bay Area (N = 1,349), HIV risk behaviors were described among the targeted API risk groups. The self-reported HIV prevalence…

Cleaning verification: Exploring the effect of the cleanliness of stainless steel surface on sample recovery.

PubMed

Haidar Ahmad, Imad A; Tam, James; Li, Xue; Duffield, William; Tarara, Thomas; Blasko, Andrei

2017-02-05

The parameters affecting the recovery of pharmaceutical residues from the surface of stainless steel coupons for quantitative cleaning verification method development have been studied, including active pharmaceutical ingredient (API) level, spiking procedure, API/excipient ratio, analyst-to-analyst variability, inter-day variability, and cleaning procedure of the coupons. The lack of a well-defined procedure that consistently cleaned coupon surface was identified as the major contributor to low and variable recoveries. Assessment of acid, base, and oxidant washes, as well as the order of treatment, showed that a base-water-acid-water-oxidizer-water wash procedure resulted in consistent, accurate spiked recovery (>90%) and reproducible results (S rel ≤4%). By applying this cleaning procedure to the previously used coupons that failed the cleaning acceptance criteria, multiple analysts were able to obtain consistent recoveries from day-to-day for different APIs, and API/excipient ratios at various spike levels. We successfully applied our approach for cleaning verification of small molecules (MW<1000Da) as well as large biomolecules (MW up to 50,000Da). Method robustness was greatly influenced by the sample preparation procedure, especially for analyses using total organic carbon (TOC) determination. Copyright © 2016 Elsevier B.V. All rights reserved.

Enabling Interoperable and Selective Data Sharing among Social Networking Sites

NASA Astrophysics Data System (ADS)

Shin, Dongwan; Lopes, Rodrigo

With the widespread use of social networking (SN) sites and even introduction of a social component in non-social oriented services, there is a growing concern over user privacy in general, how to handle and share user profiles across SN sites in particular. Although there have been several proprietary or open source-based approaches to unifying the creation of third party applications, the availability and retrieval of user profile information are still limited to the site where the third party application is run, mostly devoid of the support for data interoperability. In this paper we propose an approach to enabling interopearable and selective data sharing among SN sites. To support selective data sharing, we discuss an authenticated dictionary (ADT)-based credential which enables a user to share only a subset of her information certified by external SN sites with applications running on an SN site. For interoperable data sharing, we propose an extension to the OpenSocial API so that it can provide an open source-based framework for allowing the ADT-based credential to be used seamlessly among different SN sites.

Active pharmaceutical ingredients for antiretroviral treatment in low- and middle-income countries: a survey.

PubMed

Fortunak, Joseph M; de Souza, Rodrigo O M A; Kulkarni, Amol A; King, Christopher L; Ellison, Tiffany; Miranda, Leandro S M

2014-01-01

Active pharmaceutical ingredients (APIs) are the molecular entities that exert the therapeutic effects of medicines. This article provides an overview of the major APIs that are entered into antiretroviral therapy (ART), outlines how APIs are manufactured, and examines the regulatory and cost frameworks of manufacturing ART APIs used in low- and middle-income countries (LMICs). Almost all APIs for ART are prepared by chemical synthesis. Roughly 15 APIs account for essentially all of the ARTs used in LMICs. Nearly all of the ART APIs purchased through the Global Fund for AIDS, TB and Malaria (GFATM) or the United States President's Emergency Plan for AIDS Relief (PEPFAR) are produced by generic companies. API costs are very important because they are the largest contribution to the overall cost of ART. Efficient API production requires substantial investment in chemical manufacturing technologies and the ready availability of raw materials and energy at competitive prices. Generic API production is practiced in only a limited number of countries; the API market for ART is dominated by Indian companies. The quality of these APIs is ensured by manufacturing under good manufacturing practice (GMP), including process validation, testing against previously established specifications and the demonstration of clinical bioequivalence. The investment and personnel costs of a quality management system for GMP contribute significantly to the cost of API production. Chinese companies are the major suppliers for many advanced intermediates in API production. Improved chemistry of manufacturing, economies of scale and optimization of procurement have enabled drastic cost reductions for many ART APIs. The available capacity for global production of quality-assured APIs is likely adequate to meet forecasted demand for 2015. The increased use of ART for paediatric treatment, for second-line and salvage therapy, and the introduction of new APIs and combinations are important factors for the future of treatment in LMICs. The introduction of new fixed-dose combinations for ART and use of new drug delivery technologies could plausibly provide robust, durable ART for all patients in need, at an overall cost that is only moderately higher than what is presently being spent.

Active pharmaceutical ingredients for antiretroviral treatment in low- and middle-income countries: a survey

PubMed Central

Fortunak, Joseph M; de Souza, Rodrigo OMA; Kulkarni, Amol A; King, Christopher L; Ellison, Tiffany; Miranda, Leandro SM

2015-01-01

Active pharmaceutical ingredients (APIs) are the molecular entities that exert the therapeutic effects of medicines. This article provides an overview of the major APIs that are entered into antiretroviral therapy (ART), outlines how APIs are manufactured, and examines the regulatory and cost frameworks of manufacturing ART APIs used in low- and middle-income countries (LMICs). Almost all APIs for ART are prepared by chemical synthesis. Roughly 15 APIs account for essentially all of the ARTs used in LMICs. Nearly all of the ART APIs purchased through the Global Fund for AIDS, TB and Malaria (GFATM) or the United States President’s Emergency Plan for AIDS Relief (PEPFAR) are produced by generic companies. API costs are very important because they are the largest contribution to the overall cost of ART. Efficient API production requires substantial investment in chemical manufacturing technologies and the ready availability of raw materials and energy at competitive prices. Generic API production is practiced in only a limited number of countries; the API market for ART is dominated by Indian companies. The quality of these APIs is ensured by manufacturing under good manufacturing practice (GMP), including process validation, testing against previously established specifications and the demonstration of clinical bioequivalence. The investment and personnel costs of a quality management system for GMP contribute significantly to the cost of API production. Chinese companies are the major suppliers for many advanced intermediates in API production. Improved chemistry of manufacturing, economies of scale and optimization of procurement have enabled drastic cost reductions for many ART APIs. The available capacity for global production of quality-assured APIs is likely adequate to meet forecasted demand for 2015. The increased use of ART for paediatric treatment, for second-line and salvage therapy, and the introduction of new APIs and combinations are important factors for the future of treatment in LMICs. The introduction of new fixed-dose combinations for ART and use of new drug delivery technologies could plausibly provide robust, durable ART for all patients in need, at an overall cost that is only moderately higher than what is presently being spent. PMID:25310430

CSB: a Python framework for structural bioinformatics.

PubMed

Kalev, Ivan; Mechelke, Martin; Kopec, Klaus O; Holder, Thomas; Carstens, Simeon; Habeck, Michael

2012-11-15

Computational Structural Biology Toolbox (CSB) is a cross-platform Python class library for reading, storing and analyzing biomolecular structures with rich support for statistical analyses. CSB is designed for reusability and extensibility and comes with a clean, well-documented API following good object-oriented engineering practice. Stable release packages are available for download from the Python Package Index (PyPI) as well as from the project's website http://csb.codeplex.com. ivan.kalev@gmail.com or michael.habeck@tuebingen.mpg.de

Lateralization of visual learning in the honeybee.

PubMed

Letzkus, Pinar; Boeddeker, Norbert; Wood, Jeff T; Zhang, Shao-Wu; Srinivasan, Mandyam V

2008-02-23

Lateralization is a well-described phenomenon in humans and other vertebrates and there are interesting parallels across a variety of different vertebrate species. However, there are only a few studies of lateralization in invertebrates. In a recent report, we showed lateralization of olfactory learning in the honeybee (Apis mellifera). Here, we investigate lateralization of another sensory modality, vision. By training honeybees on a modified version of a visual proboscis extension reflex task, we find that bees learn a colour stimulus better with their right eye.

The tissue micro-array data exchange specification: a web based experience browsing imported data

PubMed Central

Nohle, David G; Hackman, Barbara A; Ayers, Leona W

2005-01-01

Background The AIDS and Cancer Specimen Resource (ACSR) is an HIV/AIDS tissue bank consortium sponsored by the National Cancer Institute (NCI) Division of Cancer Treatment and Diagnosis (DCTD). The ACSR offers to approved researchers HIV infected biologic samples and uninfected control tissues including tissue cores in micro-arrays (TMA) accompanied by de-identified clinical data. Researchers interested in the type and quality of TMA tissue cores and the associated clinical data need an efficient method for viewing available TMA materials. Because each of the tissue samples within a TMA has separate data including a core tissue digital image and clinical data, an organized, standard approach to producing, navigating and publishing such data is necessary. The Association for Pathology Informatics (API) extensible mark-up language (XML) TMA data exchange specification (TMA DES) proposed in April 2003 provides a common format for TMA data. Exporting TMA data into the proposed format offers an opportunity to implement the API TMA DES. Using our public BrowseTMA tool, we created a web site that organizes and cross references TMA lists, digital "virtual slide" images, TMA DES export data, linked legends and clinical details for researchers. Microsoft Excel® and Microsoft Word® are used to convert tabular clinical data and produce an XML file in the TMA DES format. The BrowseTMA tool contains Extensible Stylesheet Language Transformation (XSLT) scripts that convert XML data into Hyper-Text Mark-up Language (HTML) web pages with hyperlinks automatically added to allow rapid navigation. Results Block lists, virtual slide images, legends, clinical details and exports have been placed on the ACSR web site for 14 blocks with 1623 cores of 2.0, 1.0 and 0.6 mm sizes. Our virtual microscope can be used to view and annotate these TMA images. Researchers can readily navigate from TMA block lists to TMA legends and to clinical details for a selected tissue core. Exports for 11 blocks with 3812 cores from three other institutions were processed with the BrowseTMA tool. Fifty common data elements (CDE) from the TMA DES were used and 42 more created for site-specific data. Researchers can download TMA clinical data in the TMA DES format. Conclusion Virtual TMAs with clinical data can be viewed on the Internet by interested researchers using the BrowseTMA tool. We have organized our approach to producing, sorting, navigating and publishing TMA information to facilitate such review. We have converted Excel TMA data into TMA DES XML, and imported it and TMA DES XML from another institution into BrowseTMA to produce web pages that allow us to browse through the merged data. We proposed enhancements to the TMA DES as a result of this experience. We implemented improvements to the API TMA DES as a result of using exported data from several institutions. A document type definition was written for the API TMA DES (that optionally includes proposed enhancements). Independent validators can be used to check exports against the DTD (with or without the proposed enhancements). Linking tissue core images to readily navigable clinical data greatly improves the value of the TMA. PMID:16086837

libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience.

PubMed

Vella, Michael; Cannon, Robert C; Crook, Sharon; Davison, Andrew P; Ganapathy, Gautham; Robinson, Hugh P C; Silver, R Angus; Gleeson, Padraig

2014-01-01

NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment.

libNeuroML and PyLEMS: using Python to combine procedural and declarative modeling approaches in computational neuroscience

PubMed Central

Vella, Michael; Cannon, Robert C.; Crook, Sharon; Davison, Andrew P.; Ganapathy, Gautham; Robinson, Hugh P. C.; Silver, R. Angus; Gleeson, Padraig

2014-01-01

NeuroML is an XML-based model description language, which provides a powerful common data format for defining and exchanging models of neurons and neuronal networks. In the latest version of NeuroML, the structure and behavior of ion channel, synapse, cell, and network model descriptions are based on underlying definitions provided in LEMS, a domain-independent language for expressing hierarchical mathematical models of physical entities. While declarative approaches for describing models have led to greater exchange of model elements among software tools in computational neuroscience, a frequent criticism of XML-based languages is that they are difficult to work with directly. Here we describe two Application Programming Interfaces (APIs) written in Python (http://www.python.org), which simplify the process of developing and modifying models expressed in NeuroML and LEMS. The libNeuroML API provides a Python object model with a direct mapping to all NeuroML concepts defined by the NeuroML Schema, which facilitates reading and writing the XML equivalents. In addition, it offers a memory-efficient, array-based internal representation, which is useful for handling large-scale connectomics data. The libNeuroML API also includes support for performing common operations that are required when working with NeuroML documents. Access to the LEMS data model is provided by the PyLEMS API, which provides a Python implementation of the LEMS language, including the ability to simulate most models expressed in LEMS. Together, libNeuroML and PyLEMS provide a comprehensive solution for interacting with NeuroML models in a Python environment. PMID:24795618

The evaluation of physical properties of injection molded systems based on poly(ethylene oxide) (PEO).

PubMed

Pajander, Jari; Rensonnet, Alexia; Hietala, Sami; Rantanen, Jukka; Baldursdottir, Stefania

2017-02-25

The effect of product design parameters on the formation and properties of an injection molded solid dosage form consisting of poly(ethylene oxide)s (PEO) and two different active pharmaceutical ingredients (APIs) was studied. The product design parameters explored were melting temperature and the duration of melting, API loading degree and the molecular weight (M w ) of PEO. The solid form composition of the model APIs, theophylline and carbamazepine, was of specific interest, and its possible impact on the in vitro drug release behavior. M w of PEO had the greatest impact on the release rate of both APIs. High M w resulted in slower API release rate. Process temperature had two-fold effect with PEO 300,000g/mol. Firstly, higher process temperature transformed the crystalline part of the polymer into metastable folded form (more folded crystalline regions) and less into the more stable extended form (more extended crystalline regions), which lead to enhanced theophylline release rate. Secondly, the higher process temperature seemed to induce carbamazepine polymorphic transformation from p-monoclinic form III (carbamazepine (M)) into trigonal form II (carbamazepine (T)). The results indicated that the actual content of carbamazepine (T) affected drug release behavior more than the magnitude of transformation. Copyright © 2016 Elsevier B.V. All rights reserved.

The Proteins API: accessing key integrated protein and genome information

PubMed Central

Antunes, Ricardo; Alpi, Emanuele; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd

2017-01-01

Abstract The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to ‘talk’ to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). PMID:28383659

Relationships between response surfaces for tablet characteristics of placebo and API-containing tablets manufactured by direct compression method.

PubMed

Hayashi, Yoshihiro; Tsuji, Takahiro; Shirotori, Kaede; Oishi, Takuya; Kosugi, Atsushi; Kumada, Shungo; Hirai, Daijiro; Takayama, Kozo; Onuki, Yoshinori

2017-10-30

In this study, we evaluated the correlation between the response surfaces for the tablet characteristics of placebo and active pharmaceutical ingredient (API)-containing tablets. The quantities of lactose, cornstarch, and microcrystalline cellulose were chosen as the formulation factors. Ten tablet formulations were prepared. The tensile strength (TS) and disintegration time (DT) of tablets were measured as tablet characteristics. The response surfaces for TS and DT were estimated using a nonlinear response surface method incorporating multivariate spline interpolation, and were then compared with those of placebo tablets. A correlation was clearly observed for TS and DT of all APIs, although the value of the response surfaces for TS and DT was highly dependent on the type of API used. Based on this knowledge, the response surfaces for TS and DT of API-containing tablets were predicted from only two and four formulations using regression expression and placebo tablet data, respectively. The results from the evaluation of prediction accuracy showed that this method accurately predicted TS and DT, suggesting that it could construct a reliable response surface for TS and DT with a small number of samples. This technique assists in the effective estimation of the relationships between design variables and pharmaceutical responses during pharmaceutical development. Copyright © 2017 Elsevier B.V. All rights reserved.

The Proteins API: accessing key integrated protein and genome information.

PubMed

Nightingale, Andrew; Antunes, Ricardo; Alpi, Emanuele; Bursteinas, Borisas; Gonzales, Leonardo; Liu, Wudong; Luo, Jie; Qi, Guoying; Turner, Edd; Martin, Maria

2017-07-03

The Proteins API provides searching and programmatic access to protein and associated genomics data such as curated protein sequence positional annotations from UniProtKB, as well as mapped variation and proteomics data from large scale data sources (LSS). Using the coordinates service, researchers are able to retrieve the genomic sequence coordinates for proteins in UniProtKB. This, the LSS genomics and proteomics data for UniProt proteins is programmatically only available through this service. A Swagger UI has been implemented to provide documentation, an interface for users, with little or no programming experience, to 'talk' to the services to quickly and easily formulate queries with the services and obtain dynamically generated source code for popular programming languages, such as Java, Perl, Python and Ruby. Search results are returned as standard JSON, XML or GFF data objects. The Proteins API is a scalable, reliable, fast, easy to use RESTful services that provides a broad protein information resource for users to ask questions based upon their field of expertise and allowing them to gain an integrated overview of protein annotations available to aid their knowledge gain on proteins in biological processes. The Proteins API is available at (http://www.ebi.ac.uk/proteins/api/doc). © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

JUPITER: Joint Universal Parameter IdenTification and Evaluation of Reliability - An Application Programming Interface (API) for Model Analysis

USGS Publications Warehouse

Banta, Edward R.; Poeter, Eileen P.; Doherty, John E.; Hill, Mary C.

2006-01-01

he Joint Universal Parameter IdenTification and Evaluation of Reliability Application Programming Interface (JUPITER API) improves the computer programming resources available to those developing applications (computer programs) for model analysis.The JUPITER API consists of eleven Fortran-90 modules that provide for encapsulation of data and operations on that data. Each module contains one or more entities: data, data types, subroutines, functions, and generic interfaces. The modules do not constitute computer programs themselves; instead, they are used to construct computer programs. Such computer programs are called applications of the API. The API provides common modeling operations for use by a variety of computer applications.The models being analyzed are referred to here as process models, and may, for example, represent the physics, chemistry, and(or) biology of a field or laboratory system. Process models commonly are constructed using published models such as MODFLOW (Harbaugh et al., 2000; Harbaugh, 2005), MT3DMS (Zheng and Wang, 1996), HSPF (Bicknell et al., 1997), PRMS (Leavesley and Stannard, 1995), and many others. The process model may be accessed by a JUPITER API application as an external program, or it may be implemented as a subroutine within a JUPITER API application . In either case, execution of the model takes place in a framework designed by the application programmer. This framework can be designed to take advantage of any parallel processing capabilities possessed by the process model, as well as the parallel-processing capabilities of the JUPITER API.Model analyses for which the JUPITER API could be useful include, for example: Compare model results to observed values to determine how well the model reproduces system processes and characteristics.Use sensitivity analysis to determine the information provided by observations to parameters and predictions of interest.Determine the additional data needed to improve selected model predictions.Use calibration methods to modify parameter values and other aspects of the model.Compare predictions to regulatory limits.Quantify the uncertainty of predictions based on the results of one or many simulations using inferential or Monte Carlo methods.Determine how to manage the system to achieve stated objectives.The capabilities provided by the JUPITER API include, for example, communication with process models, parallel computations, compressed storage of matrices, and flexible input capabilities. The input capabilities use input blocks suitable for lists or arrays of data. The input blocks needed for one application can be included within one data file or distributed among many files. Data exchange between different JUPITER API applications or between applications and other programs is supported by data-exchange files.The JUPITER API has already been used to construct a number of applications. Three simple example applications are presented in this report. More complicated applications include the universal inverse code UCODE_2005 (Poeter et al., 2005), the multi-model analysis MMA (Eileen P. Poeter, Mary C. Hill, E.R. Banta, S.W. Mehl, and Steen Christensen, written commun., 2006), and a code named OPR_PPR (Matthew J. Tonkin, Claire R. Tiedeman, Mary C. Hill, and D. Matthew Ely, written communication, 2006).This report describes a set of underlying organizational concepts and complete specifics about the JUPITER API. While understanding the organizational concept presented is useful to understanding the modules, other organizational concepts can be used in applications constructed using the JUPITER API.

IgE-Api m 4 Is Useful for Identifying a Particular Phenotype of Bee Venom Allergy.

PubMed

Ruiz, B; Serrano, P; Moreno, C

Different clinical behaviors have been identified in patients allergic to bee venom. Compound-resolved diagnosis could be an appropriate tool for investigating these differences. The aims of this study were to analyze whether specific IgE to Api m 4 (sIgE-Api m 4) can identify a particular kind of bee venom allergy and to describe response to bee venom immunotherapy (bVIT). Prospective study of 31 patients allergic to bee venom who were assigned to phenotype group A (sIgE-Api m 4 <0.98 kU/L), treated with native aqueous (NA) extract, or phenotype group B (sIgE-Api m 4 ≥0.98 kU/L), treated with purified aqueous (PA) extract. Sex, age, cardiovascular risk, severity of preceding sting reaction, exposure to beekeeping, and immunological data (intradermal test, sIgE/sIgG4-Apis-nApi m 1, and sIgE-rApi m 2-Api m 4 were analyzed. Systemic reactions (SRs) during bVIT build-up were analyzed. Immunological and sting challenge outcomes were evaluated in each group after 1 and 2 years of bVIT. Phenotype B patients had more severe reactions (P=.049) and higher skin sensitivity (P=.011), baseline sIgE-Apis (P=.0004), sIgE-nApi m 1 (P=.0004), and sIgG4-Apis (P=.027) than phenotype A patients. Furthermore, 41% of patients in group B experienced SRs during the build-up phase with NA; the sting challenge success rate in this group was 82%. There were no significant reductions in serial intradermal test results, but an intense reduction in sIgE-nApi m 1 (P=.013) and sIgE-Api m 4 (P=.004) was observed after the first year of bVIT. Use of IgE-Api m 4 as the only discrimination criterion demonstrated differences in bee venom allergy. Further investigation with larger populations is necessary.

Chimeras of Bet v 1 and Api g 1 reveal heterogeneous IgE responses in patients with birch pollen allergy

PubMed Central

Gepp, Barbara; Lengger, Nina; Bublin, Merima; Hemmer, Wolfgang; Breiteneder, Heimo; Radauer, Christian

2014-01-01

Background Characterization of IgE-binding epitopes of allergens and determination of their patient-specific relevance is crucial for the diagnosis and treatment of allergy. Objective We sought to assess the contribution of specific surface areas of the major birch pollen allergen Bet v 1.0101 to binding IgE of individual patients. Methods Four distinct areas of Bet v 1 representing in total 81% of its surface were grafted onto the scaffold of its homolog, Api g 1.0101, to yield the chimeras Api-Bet-1 to Api-Bet-4. The chimeras were expressed in Escherichia coli and purified. IgE binding of 64 sera from Bet v 1–sensitized subjects with birch pollen allergy was determined by using direct ELISA. Specificity was assessed by means of inhibition ELISA. Results rApi g 1.0101, Api-Bet-1, Api-Bet-2, Api-Bet-3, and Api-Bet-4 bound IgE from 44%, 89%, 80%, 78%, and 48% of the patients, respectively. By comparing the amount of IgE binding to the chimeras and to rApi g 1.0101, 81%, 70%, 75%, and 45% of the patients showed significantly enhanced IgE binding to Api-Bet-1, Api-Bet-2, Api-Bet-3, and Api-Bet-4, respectively. The minority (8%) of the sera revealed enhanced IgE binding exclusively to a single chimera, whereas 31% showed increased IgE binding to all 4 chimeras compared with rApi g 1.0101. The chimeras inhibited up to 70% of IgE binding to rBet v 1.0101, confirming the specific IgE recognition of the grafted regions. Conclusion The Bet v 1–specific IgE response is polyclonal, and epitopes are spread across the entire Bet v 1 surface. Furthermore, the IgE recognition profile of Bet v 1 is highly patient specific. PMID:24529686

Predominant Api m 10 sensitization as risk factor for treatment failure in honey bee venom immunotherapy.

PubMed

Frick, Marcel; Fischer, Jörg; Helbling, Arthur; Ruëff, Franziska; Wieczorek, Dorothea; Ollert, Markus; Pfützner, Wolfgang; Müller, Sabine; Huss-Marp, Johannes; Dorn, Britta; Biedermann, Tilo; Lidholm, Jonas; Ruecker, Gerta; Bantleon, Frank; Miehe, Michaela; Spillner, Edzard; Jakob, Thilo

2016-12-01

Component resolution recently identified distinct sensitization profiles in honey bee venom (HBV) allergy, some of which were dominated by specific IgE to Api m 3 and/or Api m 10, which have been reported to be underrepresented in therapeutic HBV preparations. We performed a retrospective analysis of component-resolved sensitization profiles in HBV-allergic patients and association with treatment outcome. HBV-allergic patients who had undergone controlled honey bee sting challenge after at least 6 months of HBV immunotherapy (n = 115) were included and classified as responder (n = 79) or treatment failure (n = 36) on the basis of absence or presence of systemic allergic reactions upon sting challenge. IgE reactivity to a panel of HBV allergens was analyzed in sera obtained before immunotherapy and before sting challenge. No differences were observed between responders and nonresponders regarding levels of IgE sensitization to Api m 1, Api m 2, Api m 3, and Api m 5. In contrast, Api m 10 specific IgE was moderately but significantly increased in nonresponders. Predominant Api m 10 sensitization (>50% of specific IgE to HBV) was the best discriminator (specificity, 95%; sensitivity, 25%) with an odds ratio of 8.444 (2.127-33.53; P = .0013) for treatment failure. Some but not all therapeutic HBV preparations displayed a lack of Api m 10, whereas Api m 1 and Api m 3 immunoreactivity was comparable to that of crude HBV. In line with this, significant Api m 10 sIgG 4 induction was observed only in those patients who were treated with HBV in which Api m 10 was detectable. Component-resolved sensitization profiles in HBV allergy suggest predominant IgE sensitization to Api m 10 as a risk factor for treatment failure in HBV immunotherapy. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

Chimeras of Bet v 1 and Api g 1 reveal heterogeneous IgE responses in patients with birch pollen allergy.

PubMed

Gepp, Barbara; Lengger, Nina; Bublin, Merima; Hemmer, Wolfgang; Breiteneder, Heimo; Radauer, Christian

2014-07-01

Characterization of IgE-binding epitopes of allergens and determination of their patient-specific relevance is crucial for the diagnosis and treatment of allergy. We sought to assess the contribution of specific surface areas of the major birch pollen allergen Bet v 1.0101 to binding IgE of individual patients. Four distinct areas of Bet v 1 representing in total 81% of its surface were grafted onto the scaffold of its homolog, Api g 1.0101, to yield the chimeras Api-Bet-1 to Api-Bet-4. The chimeras were expressed in Escherichia coli and purified. IgE binding of 64 sera from Bet v 1-sensitized subjects with birch pollen allergy was determined by using direct ELISA. Specificity was assessed by means of inhibition ELISA. rApi g 1.0101, Api-Bet-1, Api-Bet-2, Api-Bet-3, and Api-Bet-4 bound IgE from 44%, 89%, 80%, 78%, and 48% of the patients, respectively. By comparing the amount of IgE binding to the chimeras and to rApi g 1.0101, 81%, 70%, 75%, and 45% of the patients showed significantly enhanced IgE binding to Api-Bet-1, Api-Bet-2, Api-Bet-3, and Api-Bet-4, respectively. The minority (8%) of the sera revealed enhanced IgE binding exclusively to a single chimera, whereas 31% showed increased IgE binding to all 4 chimeras compared with rApi g 1.0101. The chimeras inhibited up to 70% of IgE binding to rBet v 1.0101, confirming the specific IgE recognition of the grafted regions. The Bet v 1-specific IgE response is polyclonal, and epitopes are spread across the entire Bet v 1 surface. Furthermore, the IgE recognition profile of Bet v 1 is highly patient specific. Copyright © 2014 The Authors. Published by Mosby, Inc. All rights reserved.

Patient autonomy preferences among hypertensive outpatients in a primary care setting in Japan.

PubMed

Nomura, Kyoko; Ohno, Maiko; Fujinuma, Yasuki; Ishikawa, Hirono

2007-01-01

To investigate autonomy preferences and the factors to promote active patient participation in a primary care setting in Japan. Ninety-two hypertensive outpatients who consecutively visited a Japanese hospital between January and May of 2005 in Tokyo, Japan. This cross-sectional study was conducted by using a self-administered questionnaire. The main outcome measures were patient preferences for autonomy (i.e., decision-making and information-seeking preferences), measured by the Autonomy Preference Index (API). The variables studied were patient sociodemographic characteristics, physician characteristics based on patient preference (i.e., ability to communicate, extent of clinical experience, qualifications, educational background, gender, and age), and the Multidimensional Health Locus of Control. On the API scale from 0 to 100, the patients had an intermediate desire for decision-making (median: 51) and a greater desire for information (median: 95). A multivariate regression model indicated that decision-making preference increased when patients were woman and decreased as physician age increased, and information-seeking preference was positively associated with good communication skills, more extensive clinical experience, physicians of middle age, and patient beliefs that they were responsible for their own health, and was negatively associated with a preference for man physicians. Physicians may need to understand that patient autonomy preferences pertain to physician age and gender, physician communication ability and extent of clinical experience, and patient beliefs about self-responsibility toward health, and could use the information to promote reliable patient-physician relationships.

A fifth major genetic group among honeybees revealed in Syria.

PubMed

Alburaki, Mohamed; Bertrand, Bénédicte; Legout, Hélène; Moulin, Sibyle; Alburaki, Ali; Sheppard, Walter Steven; Garnery, Lionel

2013-12-06

Apiculture has been practiced in North Africa and the Middle-East from antiquity. Several thousand years of selective breeding have left a mosaic of Apis mellifera subspecies in the Middle-East, many uniquely adapted and survived to local environmental conditions. In this study we explore the genetic diversity of A. mellifera from Syria (n = 1258), Lebanon (n = 169) and Iraq (n = 35) based on 14 short tandem repeat (STR) loci in the context of reference populations from throughout the Old World (n = 732). Our data suggest that the Syrian honeybee Apis mellifera syriaca occurs in both Syrian and Lebanese territories, with no significant genetic variability between respective populations from Syria and Lebanon. All studied populations clustered within a new fifth independent nuclear cluster, congruent with an mtDNA Z haplotype identified in a previous study. Syrian honeybee populations are not associated with Oriental lineage O, except for sporadic introgression into some populations close to the Turkish and Iraqi borders. Southern Syrian and Lebanese populations demonstrated high levels of genetic diversity compared to the northern populations. This study revealed the effects of foreign queen importations on Syrian bee populations, especially for the region of Tartus, where extensive introgression of A. m. anatolica and/or A. m. caucasica alleles were identified. The policy of creating genetic conservation centers for the Syrian subspecies should take into consideration the influence of the oriental lineage O from the northern Syrian border and the large population of genetically divergent indigenous honeybees located in southern Syria.

The significance of different health institutions and their respective contributions of active pharmaceutical ingredients to wastewater.

PubMed

Herrmann, Manuel; Olsson, Oliver; Fiehn, Rainer; Herrel, Markus; Kümmerer, Klaus

2015-12-01

Active pharmaceutical ingredients (APIs) have been frequently found in the environment. It is, however, still not quite clear who is mainly responsible for API emissions. Hospitals have been considered to be the main contributing point sources for wastewater (WW) discharge of APIs. However, recent studies have shown that the contribution of hospitals to the input of APIs into the aquatic environment is quite low. Due to demographic change and the increase of psychiatric diseases, health institutions (HIs) such as psychiatric hospitals and nursing homes are likely to be important sources as well, but no data is available in this respect. This study aims to assess the impact of HIs and to provide a methodology to measure their respective contributions. Drawing on pharmaceutical consumption data for the years 2010, 2011, and 2012, this study identified API usage patterns for a psychiatric hospital (146 beds), a nursing home (286 inhabitants), and a general hospital (741 beds), the latter of which comprises three separate locations. All the HIs are located in two sub-regions of a county district with about 400,000 citizens in southwestern Germany. A selection of neurological drugs was quantified in the sewer of these facilities to evaluate the correlation between consumption and emission. The API contribution of HIs was assessed by comparing the specific consumption in the facilities with the consumption in households, expressed as the emission potential (IEP). The study shows that the usage patterns of APIs in the psychiatric hospital and the nursing home were different from the general hospital. Neurological drugs such as anticonvulsants, psycholeptics, and psychoanaleptics were mainly consumed in the psychiatric hospital and the nursing home (74% and 65%, respectively). Predicted and average measured concentrations in the effluent of the investigated HIs differed mostly by less than one order of magnitude. Therefore, the consumption-based approach is a useful method to assess usage patterns of APIs in HIs and to predict their respective contributions to WW. The national contribution of HIs on total WW discharge of APIs compared to households was very low. Only the results for the sedative clomethiazole in general hospitals as well as the antidepressant moclobemide and the antipsychotic quetiapine for the nursing homes were found to deserve some attention. The regional comparison showed that in sub-regions with a comparably higher density of HIs, the allocated facilities could be seen as point sources emitting particular APIs. However, in general, the bulk of the consumed pharmaceuticals to WW discharge has to be attributed to households. Copyright © 2015 Elsevier Ltd. All rights reserved.

Oral biopharmaceutics tools - time for a new initiative - an introduction to the IMI project OrBiTo.

PubMed

Lennernäs, H; Aarons, L; Augustijns, P; Beato, S; Bolger, M; Box, K; Brewster, M; Butler, J; Dressman, J; Holm, R; Julia Frank, K; Kendall, R; Langguth, P; Sydor, J; Lindahl, A; McAllister, M; Muenster, U; Müllertz, A; Ojala, K; Pepin, X; Reppas, C; Rostami-Hodjegan, A; Verwei, M; Weitschies, W; Wilson, C; Karlsson, C; Abrahamsson, B

2014-06-16

OrBiTo is a new European project within the IMI programme in the area of oral biopharmaceutics tools that includes world leading scientists from nine European universities, one regulatory agency, one non-profit research organization, four SMEs together with scientists from twelve pharmaceutical companies. The OrBiTo project will address key gaps in our knowledge of gastrointestinal (GI) drug absorption and deliver a framework for rational application of predictive biopharmaceutics tools for oral drug delivery. This will be achieved through novel prospective investigations to define new methodologies as well as refinement of existing tools. Extensive validation of novel and existing biopharmaceutics tools will be performed using active pharmaceutical ingredient (API), formulations and supporting datasets from industry partners. A combination of high quality in vitro or in silico characterizations of API and formulations will be integrated into physiologically based in silico biopharmaceutics models capturing the full complexity of GI drug absorption. This approach gives an unparalleled opportunity to initiate a transformational change in industrial research and development to achieve model-based pharmaceutical product development in accordance with the Quality by Design concept. Benefits include an accelerated and more efficient drug candidate selection, formulation development process, particularly for challenging projects such as low solubility molecules (BCS II and IV), enhanced and modified-release formulations, as well as allowing optimization of clinical product performance for patient benefit. In addition, the tools emerging from OrBiTo are expected to significantly reduce demand for animal experiments in the future as well as reducing the number of human bioequivalence studies required to bridge formulations after manufacturing or composition changes. Copyright © 2013 Elsevier B.V. All rights reserved.

Temporal and spatial behavior of pharmaceuticals in ...

EPA Pesticide Factsheets

The behavior of active pharmaceutical ingredients (APIs) in urban estuaries is not well understood. In this study, 15 high volume usage APIs were measured over a one year period throughout Narragansett Bay, RI, USA to determine factors controlling their concentration and distribution. Dissolved APIs ranged in concentration from not detected to 310 ng/L, with numerous APIs present at all sites and sampling periods. Eight APIs were present in suspended particulate material, ranging in concentration from <1 ng/g to 44 ng/g. Partitioning coefficients (Kds) were determined for APIs present in both the dissolved and particulate phases, with their range and variability remaining relatively constant during the study. Organic carbon normalization reduced the observed variability of several APIs to a small extent; however, other factors appear to play a role in controlling partitioning behavior. The continuous discharge of wastewater treatment plant effluents into upper Narragansett Bay resulted in sustained levels of APIs, resulting in a zone of “pseudo-persistence.” For most of the APIs, there was a strong relationship with salinity, indicating conservative behavior within the estuary. Short flushing times in Narragansett Bay coupled with APIs present primarily in the dissolved phase suggests that most APIs will be diluted and transported out of the estuary, with only small amounts of several compounds removed to and sequestered in sediments. This study ide

49 CFR 195.565 - How do I install cathodic protection on breakout tanks?

Code of Federal Regulations, 2011 CFR

2011-10-01

...) capacity built to API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the system in accordance with API Recommended Practice 651. However, installation of the system need not comply with API Recommended Practice 651 on any tank for which you note in...

49 CFR 195.579 - What must I do to mitigate internal corrosion?

Code of Federal Regulations, 2012 CFR

2012-10-01

... API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the lining in accordance with API Recommended Practice 652. However, installation of the lining need not comply with API Recommended Practice 652 on any tank for which you note in the corrosion...

49 CFR 195.565 - How do I install cathodic protection on breakout tanks?

Code of Federal Regulations, 2014 CFR

2014-10-01

...) capacity built to API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the system in accordance with API Recommended Practice 651. However, installation of the system need not comply with API Recommended Practice 651 on any tank for which you note in...

49 CFR 195.565 - How do I install cathodic protection on breakout tanks?

Code of Federal Regulations, 2013 CFR

2013-10-01

...) capacity built to API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the system in accordance with API Recommended Practice 651. However, installation of the system need not comply with API Recommended Practice 651 on any tank for which you note in...

49 CFR 195.579 - What must I do to mitigate internal corrosion?

Code of Federal Regulations, 2010 CFR

2010-10-01

... API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the lining in accordance with API Recommended Practice 652. However, installation of the lining need not comply with API Recommended Practice 652 on any tank for which you note in the corrosion...

49 CFR 195.579 - What must I do to mitigate internal corrosion?

Code of Federal Regulations, 2013 CFR

2013-10-01

... API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the lining in accordance with API Recommended Practice 652. However, installation of the lining need not comply with API Recommended Practice 652 on any tank for which you note in the corrosion...

49 CFR 195.579 - What must I do to mitigate internal corrosion?

Code of Federal Regulations, 2011 CFR

2011-10-01

... API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the lining in accordance with API Recommended Practice 652. However, installation of the lining need not comply with API Recommended Practice 652 on any tank for which you note in the corrosion...

78 FR 48738 - Self-Regulatory Organizations; C2 Options Exchange, Incorporated; Notice of Filing and Immediate...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-08-09

... depend upon the Application Programming Interface (``API'') a Permit Holder is using.\\4\\ Currently, the Exchange offers two APIs: CBOE Market Interface (``CMi'') API and Financial Information eXchange (``FIX... available APIs, and if applicable, which version, it would like to use. \\4\\ An API is a computer interface...

49 CFR 195.565 - How do I install cathodic protection on breakout tanks?

Code of Federal Regulations, 2012 CFR

2012-10-01

...) capacity built to API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the system in accordance with API Recommended Practice 651. However, installation of the system need not comply with API Recommended Practice 651 on any tank for which you note in...

49 CFR 195.579 - What must I do to mitigate internal corrosion?

Code of Federal Regulations, 2014 CFR

2014-10-01

... API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the lining in accordance with API Recommended Practice 652. However, installation of the lining need not comply with API Recommended Practice 652 on any tank for which you note in the corrosion...

49 CFR 195.565 - How do I install cathodic protection on breakout tanks?

Code of Federal Regulations, 2010 CFR

2010-10-01

...) capacity built to API Specification 12F, API Standard 620, or API Standard 650 (or its predecessor Standard 12C), you must install the system in accordance with API Recommended Practice 651. However, installation of the system need not comply with API Recommended Practice 651 on any tank for which you note in...

Limited Influence of Excipients in Extemporaneous Compounded Suspensions

PubMed Central

Dijkers, Eli; Nanhekhan, Valerie; Thorissen, Astrid; Marro, Diego; Uriel, Marta

2017-01-01

Objective: The objective of this study was to identify whether compounding oral suspensions with SyrSpend SF based on tablets or capsules is a suitable alternative for using raw pharmaceutical materials. Methods: Suspensions based on 5 different tablets and capsules were studied in SyrSpend SF. The summary of product characteristics of these different tablets and capsules were obtained from the manufacturer. Our hypothesis was that, if the maximum beyond-use date of the study was reached, the excipient did not seem to have an influence on the stability of the active pharmaceutical ingredient (API) within the studied time frame. Results: All excipients used in flecainide acetate, labetalol HCl, and tiagabine HCl tablets as well as in celecoxib and oseltamivir capsules did not seem to influence the beyond-use date of the overall suspension based on SyrSpend SF. Conclusion: Although using raw materials as API sources is preferred, oral suspensions with SyrSpend SF prepared from crushed tablets or opened capsules could be a possible alternative. Based on this study, a wide range of different excipients does not seem to impact the beyond-use date of different APIs compounded in SyrSpend SF. PMID:29276267

Limited Influence of Excipients in Extemporaneous Compounded Suspensions.

PubMed

Dijkers, Eli; Nanhekhan, Valerie; Thorissen, Astrid; Marro, Diego; Uriel, Marta

2017-06-01

Objective: The objective of this study was to identify whether compounding oral suspensions with SyrSpend SF based on tablets or capsules is a suitable alternative for using raw pharmaceutical materials. Methods: Suspensions based on 5 different tablets and capsules were studied in SyrSpend SF. The summary of product characteristics of these different tablets and capsules were obtained from the manufacturer. Our hypothesis was that, if the maximum beyond-use date of the study was reached, the excipient did not seem to have an influence on the stability of the active pharmaceutical ingredient (API) within the studied time frame. Results: All excipients used in flecainide acetate, labetalol HCl, and tiagabine HCl tablets as well as in celecoxib and oseltamivir capsules did not seem to influence the beyond-use date of the overall suspension based on SyrSpend SF. Conclusion: Although using raw materials as API sources is preferred, oral suspensions with SyrSpend SF prepared from crushed tablets or opened capsules could be a possible alternative. Based on this study, a wide range of different excipients does not seem to impact the beyond-use date of different APIs compounded in SyrSpend SF.

49 CFR 194.105 - Worst case discharge.

Code of Federal Regulations, 2013 CFR

2013-10-01

...: Prevention measure Standard Credit(percent) Secondary containment >100% NFPA 30 50 Built/repaired to API standards API STD 620/650/653 10 Overfill protection standards API RP 2350 5 Testing/cathodic protection API...

49 CFR 194.105 - Worst case discharge.

Code of Federal Regulations, 2010 CFR

2010-10-01

...: Prevention measure Standard Credit(percent) Secondary containment > 100% NFPA 30 50 Built/repaired to API standards API STD 620/650/653 10 Overfill protection standards API RP 2350 5 Testing/cathodic protection API...

49 CFR 194.105 - Worst case discharge.

Code of Federal Regulations, 2014 CFR

2014-10-01

...: Prevention measure Standard Credit(percent) Secondary containment >100% NFPA 30 50 Built/repaired to API standards API STD 620/650/653 10 Overfill protection standards API RP 2350 5 Testing/cathodic protection API...

49 CFR 194.105 - Worst case discharge.

Code of Federal Regulations, 2012 CFR

2012-10-01

...: Prevention measure Standard Credit(percent) Secondary containment > 100% NFPA 30 50 Built/repaired to API standards API STD 620/650/653 10 Overfill protection standards API RP 2350 5 Testing/cathodic protection API...

49 CFR 194.105 - Worst case discharge.

Code of Federal Regulations, 2011 CFR

2011-10-01

...: Prevention measure Standard Credit(percent) Secondary containment > 100% NFPA 30 50 Built/repaired to API standards API STD 620/650/653 10 Overfill protection standards API RP 2350 5 Testing/cathodic protection API...

The novel Akt inhibitor API-1 induces c-FLIP degradation and synergizes with TRAIL to augment apoptosis independent of Akt inhibition

PubMed Central

Li, Bo; Ren, Hui; Yue, Ping; Chen, Mingwei; Khuri, Fadlo R.; Sun, Shi-Yong

2012-01-01

API-1 is a novel small molecule inhibitor of Akt, which acts by binding to Akt and preventing its membrane translocation, and has promising preclinical antitumor activity. In this study, we reveal a novel function of API-1 in regulation of c-FLIP levels and tumor necrosis factor-related apoptosis-inducing ligand (TRAIL)-induced apoptosis, independent of Akt inhibition. API-1 effectively induced apoptosis in tested cancer cell lines including activation of caspase-8 and caspase-9. It reduced the levels of c-FLIP without increasing the expression of DR4 or DR5. Accordingly, it synergized with TRAIL to induce apoptosis. Enforced expression of ectopic c-FLIP did not attenuate API-1-induced apoptosis, but inhibited its ability to enhance TRAIL-induced apoptosis. These data indicate that downregulation of c-FLIP mediates enhancement of TRAIL-induced apoptosis by API-1, but is not sufficient for API-1-induced apoptosis. API-1-induced reduction of c-FLIP could be blocked by the proteasome inhibitor MG132. Moreover, API-1 increased c-FLIP ubiquitination and decreased c-FLIP stability. These data together suggest that API-1 downregulates c-FLIP by facilitating its ubiquitination and proteasome-mediated degradation. Since other Akt inhibitors including API-2 and MK2206 had minimal effects on reducing c-FLIP and enhancement of TRAIL-induced apoptosis, it is likely that API-1 reduces c-FLIP and enhances TRAIL-induced apoptosis independent of its Akt-inhibitory activity. PMID:22345097

Hemolymph proteome changes during worker brood development match the biological divergences between western honey bees (Apis mellifera) and eastern honey bees (Apis cerana).

PubMed

Feng, Mao; Ramadan, Haitham; Han, Bin; Fang, Yu; Li, Jianke

2014-07-05

Hemolymph plays key roles in honey bee molecule transport, immune defense, and in monitoring the physiological condition. There is a lack of knowledge regarding how the proteome achieves these biological missions for both the western and eastern honey bees (Apis mellifera and Apis cerana). A time-resolved proteome was compared using two-dimensional electrophoresis-based proteomics to reveal the mechanistic differences by analysis of hemolymph proteome changes between the worker bees of two bee species during the larval to pupal stages. The brood body weight of Apis mellifera was significantly heavier than that of Apis cerana at each developmental stage. Significantly, different protein expression patterns and metabolic pathways were observed in 74 proteins (166 spots) that were differentially abundant between the two bee species. The function of hemolymph in energy storage, odor communication, and antioxidation is of equal importance for the western and eastern bees, indicated by the enhanced expression of different protein species. However, stronger expression of protein folding, cytoskeletal and developmental proteins, and more highly activated energy producing pathways in western bees suggests that the different bee species have developed unique strategies to match their specific physiology using hemolymph to deliver nutrients and in immune defense. Our disparate findings constitute a proof-of-concept of molecular details that the ecologically shaped different physiological conditions of different bee species match with the hemolymph proteome during the brood stage. This also provides a starting point for future research on the specific hemolymph proteins or pathways related to the differential phenotypes or physiology.

Widespread dispersal of the microsporidian Nosema ceranae, an emergent pathogen of the western honey bee, Apis mellifera.

PubMed

Klee, Julia; Besana, Andrea M; Genersch, Elke; Gisder, Sebastian; Nanetti, Antonio; Tam, Dinh Quyet; Chinh, Tong Xuan; Puerta, Francisco; Ruz, José Maria; Kryger, Per; Message, Dejair; Hatjina, Fani; Korpela, Seppo; Fries, Ingemar; Paxton, Robert J

2007-09-01

The economically most important honey bee species, Apis mellifera, was formerly considered to be parasitized by one microsporidian, Nosema apis. Recently, [Higes, M., Martín, R., Meana, A., 2006. Nosema ceranae, a new microsporidian parasite in honeybees in Europe, J. Invertebr. Pathol. 92, 93-95] and [Huang, W.-F., Jiang, J.-H., Chen, Y.-W., Wang, C.-H., 2007. A Nosema ceranae isolate from the honeybee Apis mellifera. Apidologie 38, 30-37] used 16S (SSU) rRNA gene sequences to demonstrate the presence of Nosema ceranae in A. mellifera from Spain and Taiwan, respectively. We developed a rapid method to differentiate between N. apis and N. ceranae based on PCR-RFLPs of partial SSU rRNA. The reliability of the method was confirmed by sequencing 29 isolates from across the world (N =9 isolates gave N. apis RFLPs and sequences, N =20 isolates gave N. ceranae RFLPs and sequences; 100% correct classification). We then employed the method to analyze N =115 isolates from across the world. Our data, combined with N =36 additional published sequences demonstrate that (i) N. ceranae most likely jumped host to A. mellifera, probably within the last decade, (ii) that host colonies and individuals may be co-infected by both microsporidia species, and that (iii) N. ceranae is now a parasite of A. mellifera across most of the world. The rapid, long-distance dispersal of N. ceranae is likely due to transport of infected honey bees by commercial or hobbyist beekeepers. We discuss the implications of this emergent pathogen for worldwide beekeeping.

Considering ionic state in modeling sorption of pharmaceuticals to sewage sludge.

PubMed

Rybacka, Aleksandra; Andersson, Patrik L

2016-12-01

Information on the partitioning of chemicals between particulate matter and water in sewage treatment plants (STPs) can be used to predict their subsequent environmental fate. However, this information can be challenging to acquire, especially for pharmaceuticals that are frequently present in ionized forms. This study investigated the relationship between the ionization state of active pharmaceutical ingredients (APIs) and their partitioning between water and sludge in STPs. We also investigated the underlying mechanisms of sludge sorption by using chemical descriptors based on ionized structures, and evaluated the usefulness of these descriptors in quantitative structure-property relationship (QSPR) modeling. K D values were collected for 110 APIs, which were classified as neutral, positive, or negative at pH 7. The models with the highest performance had the R 2 Y and Q 2 values of above 0.75 and 0.65, respectively. We found that the dominant intermolecular forces governing the interactions of neutral and positively charged APIs with sludge are hydrophobic, pi-pi, and dipole-dipole interactions, whereas the interactions of negatively charged APIs with sludge were mainly governed by covalent bonding as well as ion-ion, ion-dipole, and dipole-dipole interactions; hydrophobicity-driven interactions were rather unimportant. Including charge-related descriptors improved the models' performance by 5-10%, underlining the importance of electrostatic interactions. The use of descriptors calculated for ionized structures did not improve the model statistics for positive and negative APIs, but slightly increased model performance for neutral APIs. We attribute this to a better description of neutral zwitterions. Copyright © 2016 Elsevier Ltd. All rights reserved.

Design and Implementation of KSP on the Next Generation Cryptography API

NASA Astrophysics Data System (ADS)

Lina, Zhang

With good seamless connectivity and higher safety, KSP (Key Storage Providers) is the inexorable trend of security requirements and development to take the place of CSP (Cryptographic Service Provider). But the study on KSP has just started in our country, and almost no reports of its implementation can be found. Based on the analysis of function modules and the architecture of Cryptography API (Next Generation (CNG)), this paper discusses the design and implementation of KSP (key storage providers) based on smart card in detail, and an example is also presented to illustrate how to use KSP in Windows Vista.

Adaptive runtime for a multiprocessing API

DOEpatents

Antao, Samuel F.; Bertolli, Carlo; Eichenberger, Alexandre E.; O'Brien, John K.

2016-11-15

A computer-implemented method includes selecting a runtime for executing a program. The runtime includes a first combination of feature implementations, where each feature implementation implements a feature of an application programming interface (API). Execution of the program is monitored, and the execution uses the runtime. Monitor data is generated based on the monitoring. A second combination of feature implementations are selected, by a computer processor, where the selection is based at least in part on the monitor data. The runtime is modified by activating the second combination of feature implementations to replace the first combination of feature implementations.

Adaptive runtime for a multiprocessing API

DOEpatents

Antao, Samuel F.; Bertolli, Carlo; Eichenberger, Alexandre E.; O'Brien, John K.

2016-10-11

A computer-implemented method includes selecting a runtime for executing a program. The runtime includes a first combination of feature implementations, where each feature implementation implements a feature of an application programming interface (API). Execution of the program is monitored, and the execution uses the runtime. Monitor data is generated based on the monitoring. A second combination of feature implementations are selected, by a computer processor, where the selection is based at least in part on the monitor data. The runtime is modified by activating the second combination of feature implementations to replace the first combination of feature implementations.

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

Veseli, S.

As the number of sites deploying and adopting EPICS Version 4 grows, so does the need to support PV Access from multiple languages. Especially important are the widely used scripting languages that tend to reduce both software development time and the learning curve for new users. In this paper we describe PvaPy, a Python API for the EPICS PV Access protocol and its accompanying structured data API. Rather than implementing the protocol itself in Python, PvaPy wraps the existing EPICS Version 4 C++ libraries using the Boost.Python framework. This approach allows us to benefit from the existing code base andmore » functionality, and to significantly reduce the Python API development effort. PvaPy objects are based on Python dictionaries and provide users with the ability to access even the most complex of PV Data structures in a relatively straightforward way. Its interfaces are easy to use, and include support for advanced EPICS Version 4 features such as implementation of client and server Remote Procedure Calls (RPC).« less

A Ruby API to query the Ensembl database for genomic features.

PubMed

Strozzi, Francesco; Aerts, Jan

2011-04-01

The Ensembl database makes genomic features available via its Genome Browser. It is also possible to access the underlying data through a Perl API for advanced querying. We have developed a full-featured Ruby API to the Ensembl databases, providing the same functionality as the Perl interface with additional features. A single Ruby API is used to access different releases of the Ensembl databases and is also able to query multi-species databases. Most functionality of the API is provided using the ActiveRecord pattern. The library depends on introspection to make it release independent. The API is available through the Rubygem system and can be installed with the command gem install ruby-ensembl-api.

Comparison of ground based indices (API and AQI) with satellite based aerosol products.

PubMed

Zheng, Sheng; Cao, Chun-Xiang; Singh, Ramesh P

2014-08-01

Air quality in mega cities is one of the major concerns due to serious health issues and its indirect impact to the climate. Among mega cities, Beijing city is considered as one of the densely populated cities with extremely poor air quality. The meteorological parameters (wind, surface temperature, air temperature and relative humidity) control the dynamics and dispersion of air pollution. China National Environmental Monitoring Centre (CNEMC) started air pollution index (API) as of 2000 to evaluate air quality, but over the years, it was felt that the air quality is not well represented by API. Recently, the Ministry of Environmental Protection (MEP) of the People's Republic of China (PRC) started using a new index "air quality index (AQI)" from January 2013. We have compared API and AQI with three different MODIS (MODIS - Moderate Resolution Imaging SpectroRadiometer, onboard the Terra/Aqua satellites) AOD (aerosol optical depth) products for ten months, January-October, 2013. The correlation between AQI and Aqua Deep Blue AOD was found to be reasonably good as compared with API, mainly due to inclusion of PM2.5 in the calculation of AQI. In addition, for every month, the correlation coefficient between AQI and Aqua Deep Blue AOD was found to be relatively higher in the month of February to May. According to the monthly average distribution of precipitation, temperature, and PM10, the air quality in the months of June-September was better as compared to those in the months of February-May. AQI and Aqua Deep Blue AOD show highly polluted days associated with dust event, representing true air quality of Beijing. Copyright © 2013 Elsevier B.V. All rights reserved.

49 CFR 195.205 - Repair, alteration and reconstruction of aboveground breakout tanks that have been in service.

Code of Federal Regulations, 2014 CFR

2014-10-01

...-refrigerated and tanks built to API Standard 650 or its predecessor Standard 12C, repair, alteration, and reconstruction must be in accordance with API Standard 653. (2) For tanks built to API Specification 12F or API..., examination, and material requirements of those respective standards. (3) For high pressure tanks built to API...

49 CFR 195.205 - Repair, alteration and reconstruction of aboveground breakout tanks that have been in service.

Code of Federal Regulations, 2013 CFR

2013-10-01

...-refrigerated and tanks built to API Standard 650 or its predecessor Standard 12C, repair, alteration, and reconstruction must be in accordance with API Standard 653. (2) For tanks built to API Specification 12F or API..., examination, and material requirements of those respective standards. (3) For high pressure tanks built to API...

49 CFR 195.205 - Repair, alteration and reconstruction of aboveground breakout tanks that have been in service.

Code of Federal Regulations, 2012 CFR

2012-10-01

...-refrigerated and tanks built to API Standard 650 or its predecessor Standard 12C, repair, alteration, and reconstruction must be in accordance with API Standard 653. (2) For tanks built to API Specification 12F or API..., examination, and material requirements of those respective standards. (3) For high pressure tanks built to API...

49 CFR 195.205 - Repair, alteration and reconstruction of aboveground breakout tanks that have been in service.

Code of Federal Regulations, 2011 CFR

2011-10-01

...-refrigerated and tanks built to API Standard 650 or its predecessor Standard 12C, repair, alteration, and reconstruction must be in accordance with API Standard 653. (2) For tanks built to API Specification 12F or API..., examination, and material requirements of those respective standards. (3) For high pressure tanks built to API...

Infra-Population and -Community Dynamics of the Parasites Nosema apis and Nosema ceranae, and Consequences for Honey Bee (Apis mellifera) Hosts

PubMed Central

Williams, Geoffrey R.; Shutler, Dave; Burgher-MacLellan, Karen L.; Rogers, Richard E. L.

2014-01-01

Nosema spp. fungal gut parasites are among myriad possible explanations for contemporary increased mortality of western honey bees (Apis mellifera, hereafter honey bee) in many regions of the world. Invasive Nosema ceranae is particularly worrisome because some evidence suggests it has greater virulence than its congener N. apis. N. ceranae appears to have recently switched hosts from Asian honey bees (Apis cerana) and now has a nearly global distribution in honey bees, apparently displacing N. apis. We examined parasite reproduction and effects of N. apis, N. ceranae, and mixed Nosema infections on honey bee hosts in laboratory experiments. Both infection intensity and honey bee mortality were significantly greater for N. ceranae than for N. apis or mixed infections; mixed infection resulted in mortality similar to N. apis parasitism and reduced spore intensity, possibly due to inter-specific competition. This is the first long-term laboratory study to demonstrate lethal consequences of N. apis and N. ceranae and mixed Nosema parasitism in honey bees, and suggests that differences in reproduction and intra-host competition may explain apparent heterogeneous exclusion of the historic parasite by the invasive species. PMID:24987989

Infra-population and -community dynamics of the parasites Nosema apis and Nosema ceranae, and consequences for honey bee (Apis mellifera) hosts.

PubMed

Williams, Geoffrey R; Shutler, Dave; Burgher-MacLellan, Karen L; Rogers, Richard E L

2014-01-01

Nosema spp. fungal gut parasites are among myriad possible explanations for contemporary increased mortality of western honey bees (Apis mellifera, hereafter honey bee) in many regions of the world. Invasive Nosema ceranae is particularly worrisome because some evidence suggests it has greater virulence than its congener N. apis. N. ceranae appears to have recently switched hosts from Asian honey bees (Apis cerana) and now has a nearly global distribution in honey bees, apparently displacing N. apis. We examined parasite reproduction and effects of N. apis, N. ceranae, and mixed Nosema infections on honey bee hosts in laboratory experiments. Both infection intensity and honey bee mortality were significantly greater for N. ceranae than for N. apis or mixed infections; mixed infection resulted in mortality similar to N. apis parasitism and reduced spore intensity, possibly due to inter-specific competition. This is the first long-term laboratory study to demonstrate lethal consequences of N. apis and N. ceranae and mixed Nosema parasitism in honey bees, and suggests that differences in reproduction and intra-host competition may explain apparent heterogeneous exclusion of the historic parasite by the invasive species.

Transcriptome differences in the hypopharyngeal gland between Western Honeybees (Apis mellifera) and Eastern Honeybees (Apis cerana).

PubMed

Liu, Hao; Wang, Zi-Long; Tian, Liu-Qing; Qin, Qiu-Hong; Wu, Xiao-Bo; Yan, Wei-Yu; Zeng, Zhi-Jiang

2014-08-30

Apis mellifera and Apis cerana are two sibling species of Apidae. Apis cerana is adept at collecting sporadic nectar in mountain and forest region and exhibits stiffer hardiness and acarid resistance as a result of natural selection, whereas Apis mellifera has the advantage of producing royal jelly. To identify differentially expressed genes (DEGs) that affect the development of hypopharyngeal gland (HG) and/or the secretion of royal jelly between these two honeybee species, we performed a digital gene expression (DGE) analysis of the HGs of these two species at three developmental stages (newly emerged worker, nurse and forager). Twelve DGE-tag libraries were constructed and sequenced using the total RNA extracted from the HGs of newly emerged workers, nurses, and foragers of Apis mellifera and Apis cerana. Finally, a total of 1482 genes in Apis mellifera and 1313 in Apis cerana were found to exhibit an expression difference among the three developmental stages. A total of 1417 DEGs were identified between these two species. Of these, 623, 1072, and 462 genes showed an expression difference at the newly emerged worker, nurse, and forager stages, respectively. The nurse stage exhibited the highest number of DEGs between these two species and most of these were found to be up-regulated in Apis mellifera. These results suggest that the higher yield of royal jelly in Apis mellifera may be due to the higher expression level of these DEGs. In this study, we investigated the DEGs between the HGs of two sibling honeybee species (Apis mellifera and Apis cerana). Our results indicated that the gene expression difference was associated with the difference in the royal jelly yield between these two species. These results provide an important clue for clarifying the mechanisms underlying hypopharyngeal gland development and the production of royal jelly.

The Secret Life of Quarks, Final Report for the University of North Carolina at Chapel Hill

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

Fowler, Robert J.

This final report summarizes activities and results at the University of North Carolina as part of the the SciDAC-2 Project The Secret Life of Quarks: National Computational Infrastructure for Lattice Quantum Chromodynamics. The overall objective of the project is to construct the software needed to study quantum chromo- dynamics (QCD), the theory of the strong interactions of subatomic physics, and similar strongly coupled gauge theories anticipated to be of importance in the LHC era. It built upon the successful efforts of the SciDAC-1 project National Computational Infrastructure for Lattice Gauge Theory, in which a QCD Applications Programming Interface (QCD API)more » was developed that enables lat- tice gauge theorists to make effective use of a wide variety of massively parallel computers. In the SciDAC-2 project, optimized versions of the QCD API were being created for the IBM Blue- Gene/L (BG/L) and BlueGene/P (BG/P), the Cray XT3/XT4 and its successors, and clusters based on multi-core processors and Infiniband communications networks. The QCD API is being used to enhance the performance of the major QCD community codes and to create new applications. Software libraries of physics tools have been expanded to contain sharable building blocks for inclusion in application codes, performance analysis and visualization tools, and software for au- tomation of physics work flow. New software tools were designed for managing the large data sets generated in lattice QCD simulations, and for sharing them through the International Lattice Data Grid consortium. As part of the overall project, researchers at UNC were funded through ASCR to work in three general areas. The main thrust has been performance instrumentation and analysis in support of the SciDAC QCD code base as it evolved and as it moved to new computation platforms. In support of the performance activities, performance data was to be collected in a database for the purpose of broader analysis. Third, the UNC work was done at RENCI (Renaissance Computing Institute), which has extensive expertise and facilities for scientific data visualization, so we acted in an ongoing consulting and support role in that area.« less

Peculiar surface behavior of some ionic liquids based on active pharmaceutical ingredients

NASA Astrophysics Data System (ADS)

Restolho, José; Mata, José Luis; Saramago, Benilde

2011-02-01

The ionic liquids based on biologically active cations and anions, commonly designated by ionic liquids based on active pharmaceutical ingredients (ILs-APIs), are interesting compounds for use in pharmaceutical applications. Lidocaine docusate, ranitidine docusate, and didecyldimethylammonium ibuprofen are examples of promising ILs-APIs that were recently synthesized. They were submitted to biological testing and calorimetric measurements, but nothing is known about their surface properties. In this work, we measured the surface tension and the contact angles on both hydrophilic and hydrophobic surfaces in a temperature range as wide as possible. Based on the wettability data, the polarity fractions were estimated using the Fowkes theory. The peculiar surface behavior observed was tentatively attributed to the presence of mesophases.

49 CFR 195.264 - Impoundment, protection against entry, normal/emergency venting or pressure/vacuum relief for...

Code of Federal Regulations, 2014 CFR

2014-10-01

... specified: (1) For tanks built to API Specification 12F, API Standard 620, and others (such as API Standard... accordance with section 4.3.2.3.1. (2) For tanks built to API 2510, the installation of impoundment must be in accordance with section 5 or 11 of API 2510 (incorporated by reference, see § 195.3). (c...

49 CFR 195.264 - Impoundment, protection against entry, normal/emergency venting or pressure/vacuum relief for...

Code of Federal Regulations, 2012 CFR

2012-10-01

... specified: (1) For tanks built to API Specification 12F, API Standard 620, and others (such as API Standard... accordance with section 4.3.2.3.1. (2) For tanks built to API 2510, the installation of impoundment must be in accordance with section 5 or 11 of API 2510 (incorporated by reference, see § 195.3). (c...

49 CFR 195.264 - Impoundment, protection against entry, normal/emergency venting or pressure/vacuum relief for...

Code of Federal Regulations, 2013 CFR

2013-10-01

... specified: (1) For tanks built to API Specification 12F, API Standard 620, and others (such as API Standard... accordance with section 4.3.2.3.1. (2) For tanks built to API 2510, the installation of impoundment must be in accordance with section 5 or 11 of API 2510 (incorporated by reference, see § 195.3). (c...

49 CFR 195.264 - Impoundment, protection against entry, normal/emergency venting or pressure/vacuum relief for...

Code of Federal Regulations, 2011 CFR

2011-10-01

... specified: (1) For tanks built to API Specification 12F, API Standard 620, and others (such as API Standard... accordance with section 4.3.2.3.1. (2) For tanks built to API 2510, the installation of impoundment must be in accordance with section 5 or 11 of API 2510 (incorporated by reference, see § 195.3). (c...

Continuous production of controlled release dosage forms based on hot-melt extruded gum arabic: Formulation development, in vitro characterization and evaluation of potential application fields.

PubMed

Kipping, Thomas; Rein, Hubert

2016-01-30

Controlled release matrices based on gum arabic are prepared by applying a continuous hot-melt extrusion technology: the pre-mixture consisting of gum arabic and the incorporated API is plasticized by a co-rotating twin-screw extruder, an intermediate strand is formed by a round nozzle. Single dosed matrices are prepared by cutting the semi elastic strand with a rotary fly cutter. Paracetamol and phenazone are used as model drug substances. High drug loadings up to 70% can be realized. Matrices are characterized concerning their crystalline structure, in vitro dissolution, disintegration time and various physical parameters including glass transition temperature (Tg). Release characteristic behavior is mainly influenced by erosion of the matrices. At higher drug loadings also diffusion based transport gain importance. The solubility of the API shows an influence on the erosion rate of the matrix and should therefore be considered during formulation development. Tg is mainly influenced by the solubility of the API in the surrounding matrix. High soluble phenazone shows a decrease, whereas paracetamol addition has nearly no influence on the Tg of the polymeric system. Activation energy (EA) of the glass transition is determined via dynamic mechanical analysis. The addition of APIs leads to a reduction of EA indicating an increased molecular movement at Tg region compared to placebo extrudates. X-ray diffraction is used to determine the crystalline state of the extruded matrices and interaction between matrix and incorporated APIs. The production of thin layer matrices is an interesting option to provide a fast drug delivery to the oral cavity. High mechanical strength combined with fast disintegration times can be a great advantage for the development of oro-dispersible tablets. A great benefit of the evaluated processing technology is the simple adaption of the final dose by varying either the cutting length or the diameter of the nozzle resulting in a cost-effective production of single dosed matrices without modification of the base formula. Copyright © 2015 Elsevier B.V. All rights reserved.

Enhanced performance of dye-sensitized solar cells based on organic dopant incorporated PVDF-HFP/PEO polymer blend electrolyte with g-C{sub 3}N{sub 4}/TiO{sub 2} photoanode

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

Senthil, R.A.; Theerthagiri, J.; Madhavan, J., E-mail: jagan.madhavan@gmail.com

This work describes the effect of 2-aminopyrimidine (2-APY) on poly(vinylidinefluoride-co-hexafluoropropylene) (PVDF-HFP)/polyethylene oxide (PEO) blend polymer electrolyte along with binary iodide salts (tetrabutylammonium iodide (TBAI) and potassium iodide (KI)) and iodine (I{sub 2}) were studied for enhancing the efficiency of the dye-sensitized solar cells (DSSCs) consisting of g-C{sub 3}N{sub 4}/TiO{sub 2} composite as photoanode. The g-C{sub 3}N{sub 4} was synthesized from low cost urea by thermal condensation method. It was used as a precursor to synthesize the various weight percentage ratios (5%, 10% and 15%) of g-C{sub 3}N{sub 4}/TiO{sub 2} composites by wet-impregnation method. The pure and 2-APY incorporated PVDF-HFP/PEO polymermore » blend electrolytes were arranged by wet chemical process (casting method) using DMF as a solvent. The synthesized g-C{sub 3}N{sub 4}/TiO{sub 2} composites and polymer blend electrolytes were studied and analyzed by Fourier transform infrared (FT-IR) spectroscopy, X-ray diffractometer (XRD) and scanning electron microscopy (SEM). The ionic conductivity values of the pure and 2-APY incorporated PVDF-HFP/PEO blend electrolytes were estimated to be 4.53×10{sup −5} and 1.87×10{sup −4} Scm{sup −1} respectively. The UV–vis absorption spectroscopy was carried out for the pure and different wt% of g-C{sub 3}N{sub 4}/TiO{sub 2} composites coated FTO films after N3 dye-sensitization. The 10 wt% g-C{sub 3}N{sub 4}/TiO{sub 2} composite film showed a maximum absorption compared to the others. The DSSC assembled with 10 wt% g-C{sub 3}N{sub 4}/TiO{sub 2} as photoanode using the pure polymer blend electrolyte exhibited a power conversion efficiency (PCE) of 3.17% , which was superior than that of DSSC based pure TiO{sub 2} (2.46%). However, the PCE was increased to 4.73% for the DSSC assembled using 10 wt% g-C{sub 3}N{sub 4}/TiO{sub 2} as photoanode with 2-APY incorporated polymer blend electrolyte. Hence, the present study is a successful attempt to provide a new pathway to enhance the performance of DSSCs. - Graphical abstract: In this study, the g-C{sub 3}N{sub 4} was synthesized from low cost urea and it was used as a precursor to synthesize of g-C{sub 3}N{sub 4}/TiO{sub 2} composite. The pure and 2-APY incorporated PVDF-HFP/PEO electrolytes were fabricated by solution casting method. A remarkably enhanced PCE of 4.73% was observed for 2-APY incorporated PVDF-HFP/PEO electrolyte with g-C{sub 3}N{sub 4}/TiO{sub 2} composite photoanode based DSSC. - Highlights: • 2-APY added PVDF-HFP/PEO electrolyte was prepared by solution casting method. • The g-C{sub 3}N{sub 4}/TiO{sub 2} composites were synthesized by wet-impregnation method. • DSSC with g-C{sub 3}N{sub 4}/TiO{sub 2} and 2-APY added electrolyte showed the efficiency of 4.73 %. • The g-C{sub 3}N{sub 4} and 2-APY can be a useful dopant to enhance the performance of DSSCs.« less

Calcareous microfossil-based orbital cyclostratigraphy in the Arctic Ocean

USGS Publications Warehouse

Marzen, Rachel; DeNinno, Lauren H.; Cronin, Thomas M.

2016-01-01

Microfaunal and geochemical proxies from marine sediment records from central Arctic Ocean (CAO) submarine ridges suggest a close relationship over the last 550 thousand years (kyr) between orbital-scale climatic oscillations, sea-ice cover, marine biological productivity and other parameters. Multiple paleoclimate proxies record glacial to interglacial cycles. To understand the climate-cryosphere-productivity relationship, we examined the cyclostratigraphy of calcareous microfossils and constructed a composite Arctic Paleoclimate Index (API) "stack" from benthic foraminiferal and ostracode density from 14 sediment cores. Following the hypothesis that API is driven mainly by changes in sea-ice related productivity, the API stack shows the Arctic experienced a series of highly productive interglacials and interstadials every ∼20 kyr. These periods signify minimal ice shelf and sea-ice cover and maximum marine productivity. Rapid transitions in productivity are seen during shifts from interglacial to glacial climate states. Discrepancies between the Arctic API curves and various global climatic, sea-level and ice-volume curves suggest abrupt growth and decay of Arctic ice shelves related to climatic and sea level oscillations.

Early process development of API applied to poorly water-soluble TBID.

PubMed

Meise, Marius; Niggemann, Matthias; Dunens, Alexandra; Schoenitz, Martin; Kuschnerow, Jan C; Kunick, Conrad; Scholl, Stephan

2018-05-01

Finding and optimising of synthesis processes for active pharmaceutical ingredients (API) is time consuming. In the finding phase, established methods for synthesis, purification and formulation are used to achieve a high purity API for biological studies. For promising API candidates, this is followed by pre-clinical and clinical studies requiring sufficient quantities of the active component. Ideally, these should be produced with a process representative for a later production process and suitable for scaling to production capacity. This work presents an overview of different approaches for process synthesis based on an existing lab protocol. This is demonstrated for the production of the model drug 4,5,6,7-tetrabromo-2-(1H-imidazol-2-yl) isoindolin-1,3-dione (TBID). Early batch synthesis and purification procedures typically suffer from low and fluctuating yields and purities due to poor process control. In a first step the literature synthesis and purification procedure was modified and optimized using solubility measurements, targeting easier and safer processing for consecutive studies. Copyright © 2018 Elsevier B.V. All rights reserved.

The novel Akt inhibitor API-1 induces c-FLIP degradation and synergizes with TRAIL to augment apoptosis independent of Akt inhibition.

PubMed

Li, Bo; Ren, Hui; Yue, Ping; Chen, Mingwei; Khuri, Fadlo R; Sun, Shi-Yong

2012-04-01

API-1 (pyrido[2,3-d]pyrimidines) is a novel small-molecule inhibitor of Akt, which acts by binding to Akt and preventing its membrane translocation and has promising preclinical antitumor activity. In this study, we reveal a novel function of API-1 in regulation of cellular FLICE-inhibitory protein (c-FLIP) levels and TRAIL-induced apoptosis, independent of Akt inhibition. API-1 effectively induced apoptosis in tested cancer cell lines including activation of caspase-8 and caspase-9. It reduced the levels of c-FLIP without increasing the expression of death receptor 4 (DR4) or DR5. Accordingly, it synergized with TRAIL to induce apoptosis. Enforced expression of ectopic c-FLIP did not attenuate API-1-induced apoptosis but inhibited its ability to enhance TRAIL-induced apoptosis. These data indicate that downregulation of c-FLIP mediates enhancement of TRAIL-induced apoptosis by API-1 but is not sufficient for API-1-induced apoptosis. API-1-induced reduction of c-FLIP could be blocked by the proteasome inhibitor MG132. Moreover, API-1 increased c-FLIP ubiquitination and decreased c-FLIP stability. These data together suggest that API-1 downregulates c-FLIP by facilitating its ubiquitination and proteasome-mediated degradation. Because other Akt inhibitors including API-2 and MK2206 had minimal effects on reducing c-FLIP and enhancement of TRAIL-induced apoptosis, it is likely that API-1 reduces c-FLIP and enhances TRAIL-induced apoptosis independent of its Akt-inhibitory activity. 2012 AACR

Comprehensive study of the drug delivery properties of poly(l-lactide)-poly(ethylene glycol) nanoparticles in rats and tumor-bearing mice.

PubMed

Shalgunov, Vladimir; Zaytseva-Zotova, Daria; Zintchenko, Arkadi; Levada, Tatiana; Shilov, Yuri; Andreyev, Dmitry; Dzhumashev, Dzhangar; Metelkin, Evgeny; Urusova, Alexandra; Demin, Oleg; McDonnell, Kevin; Troiano, Greg; Zale, Stephen; Safarovа, Elmira

2017-09-10

Nanoparticles made of polylactide-poly(ethylene glycol) block-copolymer (PLA-PEG) are promising vehicles for drug delivery due to their biodegradability and controllable payload release. However, published data on the drug delivery properties of PLA-PEG nanoparticles are heterogeneous in terms of nanoparticle characteristics and mostly refer to low injected doses (a few mg nanoparticles per kg body weight). We have performed a comprehensive study of the biodistribution of nanoparticle formulations based on PLA-PEG nanoparticles of ~100nm size at injected doses of 30 to 140mg/kg body weight in healthy rats and nude tumor-bearing mice. Nanoparticle formulations differed by surface PEG coverage and by release kinetics of the encapsulated model active pharmaceutical ingredient (API). Increase in PEG coverage prolonged nanoparticle circulation half-life up to ~20h in rats and ~10h in mice and decreased retention in liver, spleen and lungs. Circulation half-life of the encapsulated API grew monotonously as the release rate slowed down. Plasma and tissue pharmacokinetics was dose-linear for inactive nanoparticles, but markedly dose-dependent for the model therapeutic formulation, presumably because of the toxic effects of released API. A mathematical model of API distribution calibrated on the data for inactive nanoparticles and conventional API form correctly predicted the distribution of the model therapeutic formulation at the lowest investigated dose, but for higher doses the toxic action of the released API had to be explicitly modelled. Our results provide a coherent illustration of the ability of controllable-release PLA-PEG nanoparticles to serve as an effective drug delivery platform to alter API biodistribution. They also underscore the importance of physiological effects of released drug in determining the biodistribution of therapeutic drug formulations at doses approaching tolerability limits. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Effects of the aspartic protease inhibitor from Lupinus bogotensis seeds on the growth and development of Hypothenemus hampei: an inhibitor showing high homology with storage proteins.

PubMed

Molina, Diana; Patiño, Luisa; Quintero, Mónica; Cortes, José; Bastos, Sara

2014-02-01

The coffee berry borer Hypothenemus hampei is a pest that causes great economic damage to coffee grains worldwide. Because the proteins consumed are digested by aspartic proteases in the insect's midgut, the inhibition of these proteases by transferring a gene encoding an aspartic protease inhibitor from Lupinus bogotensis Benth. to coffee plants could provide a promising strategy to control this pest. Five aspartic protease inhibitors from L. bogotensis (LbAPI) were accordingly purified and characterized. The gene encoding the L. bogotensis aspartic protease inhibitor (LbAPI), with the highest inhibitory activity against H. hampei, was expressed in Escherichia coli and the purified recombinant protein (rLbAPI), with a molecular mass of 15 kDa, was subsequently assessed for its ability to inhibit the aspartic protease activity present in the H. hampei midgut in vitro, as well as its effects on the growth and development of H. hampei in vivo. The in vitro experiments showed that rLbAPI was highly effective against aspartic proteases from H. hampei guts, with a half maximal inhibitory concentration (IC50) of 2.9 μg. The in vivo experiments showed that the concentration of rLbAPI (w/w) in the artificial diet necessary to cause 50% mortality (LD50) of the larvae was 0.91%. The amino acid sequence of LbAPI had high homology (52-80%) to the seed storage proteins, vicilin and β-conglutin, suggesting that this protein was generated by evolutionary events from a β-conglutin precursor. Based on these results, LbAPI may have a dual function as storage protein, and as defense protein against H. hampei. These results provide a promising alternative to obtain a coffee plant resistant to H. hampei. Copyright © 2013 Elsevier Ltd. All rights reserved.

16 CFR 311.4 - Testing.

Code of Federal Regulations, 2013 CFR

2013-01-01

... (“API”), Publication 1509, Thirteenth Edition, January 1995. API Publication 1509, Thirteenth Edition has been updated to API Publication 1509, Fifteenth Edition, April 2002. API Publication 1509... the materials incorporated by reference may be obtained from: API, 1220 L Street, NW., Washington, DC...

16 CFR 311.4 - Testing.

Code of Federal Regulations, 2014 CFR

2014-01-01

... (“API”), Publication 1509, Thirteenth Edition, January 1995. API Publication 1509, Thirteenth Edition has been updated to API Publication 1509, Fifteenth Edition, April 2002. API Publication 1509... the materials incorporated by reference may be obtained from: API, 1220 L Street, NW., Washington, DC...

16 CFR 311.4 - Testing.

Code of Federal Regulations, 2012 CFR

2012-01-01

... (“API”), Publication 1509, Thirteenth Edition, January 1995. API Publication 1509, Thirteenth Edition has been updated to API Publication 1509, Fifteenth Edition, April 2002. API Publication 1509... the materials incorporated by reference may be obtained from: API, 1220 L Street, NW., Washington, DC...

16 CFR 311.4 - Testing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... (“API”), Publication 1509, Thirteenth Edition, January 1995. API Publication 1509, Thirteenth Edition has been updated to API Publication 1509, Fifteenth Edition, April 2002. API Publication 1509... the materials incorporated by reference may be obtained from: API, 1220 L Street, NW., Washington, DC...

Development of a NIR-based blend uniformity method for a drug product containing multiple structurally similar actives by using the quality by design principles.

PubMed

Lin, Yiqing; Li, Weiyong; Xu, Jin; Boulas, Pierre

2015-07-05

The aim of this study is to develop an at-line near infrared (NIR) method for the rapid and simultaneous determination of four structurally similar active pharmaceutical ingredients (APIs) in powder blends intended for the manufacturing of tablets. Two of the four APIs in the formula are present in relatively small amounts, one at 0.95% and the other at 0.57%. Such small amounts in addition to the similarity in structures add significant complexity to the blend uniformity analysis. The NIR method is developed using spectra from six laboratory-created calibration samples augmented by a small set of spectra from a large-scale blending sample. Applying the quality by design (QbD) principles, the calibration design included concentration variations of the four APIs and a main excipient, microcrystalline cellulose. A bench-top FT-NIR instrument was used to acquire the spectra. The obtained NIR spectra were analyzed by applying principal component analysis (PCA) before calibration model development. Score patterns from the PCA were analyzed to reveal relationship between latent variables and concentration variations of the APIs. In calibration model development, both PLS-1 and PLS-2 models were created and evaluated for their effectiveness in predicting API concentrations in the blending samples. The final NIR method shows satisfactory specificity and accuracy. Copyright © 2015 Elsevier B.V. All rights reserved.

An Algorithm to Identify Compounded Non-Sterile Products that Can Be Formulated on a Commercial Scale or Imported to Promote Safer Medication Use in Children

PubMed Central

Bhatt-Mehta, Varsha; MacArthur, Robert B.; Löbenberg, Raimar; Cies, Jeffrey J.; Cernak, Ibolja; Parrish, Richard H.

2015-01-01

The lack of commercially-available pediatric drug products and dosage forms is well-known. A group of clinicians and scientists with a common interest in pediatric drug development and medicines-use systems developed a practical framework for identifying a list of active pharmaceutical ingredients (APIs) with the greatest market potential for development to use in pediatric patients. Reliable and reproducible evidence-based drug formulations designed for use in pediatric patients are needed vitally, otherwise safe and consistent clinical practices and outcomes assessments will continue to be difficult to ascertain. Identification of a prioritized list of candidate APIs for oral formulation using the described algorithm provides a broader integrated clinical, scientific, regulatory, and market basis to allow for more reliable dosage forms and safer, effective medicines use in children of all ages. Group members derived a list of candidate API molecules by factoring in a number of pharmacotherapeutic, scientific, manufacturing, and regulatory variables into the selection algorithm that were absent in other rubrics. These additions will assist in identifying and categorizing prime API candidates suitable for oral formulation development. Moreover, the developed algorithm aids in prioritizing useful APIs with finished oral liquid dosage forms available from other countries with direct importation opportunities to North America and beyond. PMID:28975916

In Vitro and In Vivo Anti-tumoral Effects of the Flavonoid Apigenin in Malignant Mesothelioma

PubMed Central

Masuelli, Laura; Benvenuto, Monica; Mattera, Rosanna; Di Stefano, Enrica; Zago, Erika; Taffera, Gloria; Tresoldi, Ilaria; Giganti, Maria Gabriella; Frajese, Giovanni Vanni; Berardi, Ginevra; Modesti, Andrea; Bei, Roberto

2017-01-01

Malignant mesothelioma (MM) is a tumor arising from mesothelium. MM patients’ survival is poor. The polyphenol 4′,5,7,-trihydroxyflavone Apigenin (API) is a “multifunctional drug”. Several studies have demonstrated API anti-tumoral effects. However, little is known on the in vitro and in vivo anti-tumoral effects of API in MM. Thus, we analyzed the in vitro effects of API on cell proliferation, cell cycle regulation, pro-survival signaling pathways, apoptosis, and autophagy of human and mouse MM cells. We evaluated the in vivo anti-tumor activities of API in mice transplanted with MM #40a cells forming ascites. API inhibited in vitro MM cells survival, increased reactive oxygen species intracellular production and induced DNA damage. API activated apoptosis but not autophagy. API-induced apoptosis was sustained by the increase of Bax/Bcl-2 ratio, increase of p53 expression, activation of both caspase 9 and caspase 8, cleavage of PARP-1, and increase of the percentage of cells in subG1 phase. API treatment affected the phosphorylation of ERK1/2, JNK and p38 MAPKs in a cell-type specific manner, inhibited AKT phosphorylation, decreased c-Jun expression and phosphorylation, and inhibited NF-κB nuclear translocation. Intraperitoneal administration of API increased the median survival of C57BL/6 mice intraperitoneally transplanted with #40a cells and reduced the risk of tumor growth. Our findings may have important implications for the design of MM treatment using API. PMID:28674496

A parallel solver for huge dense linear systems

NASA Astrophysics Data System (ADS)

Badia, J. M.; Movilla, J. L.; Climente, J. I.; Castillo, M.; Marqués, M.; Mayo, R.; Quintana-Ortí, E. S.; Planelles, J.

2011-11-01

HDSS (Huge Dense Linear System Solver) is a Fortran Application Programming Interface (API) to facilitate the parallel solution of very large dense systems to scientists and engineers. The API makes use of parallelism to yield an efficient solution of the systems on a wide range of parallel platforms, from clusters of processors to massively parallel multiprocessors. It exploits out-of-core strategies to leverage the secondary memory in order to solve huge linear systems O(100.000). The API is based on the parallel linear algebra library PLAPACK, and on its Out-Of-Core (OOC) extension POOCLAPACK. Both PLAPACK and POOCLAPACK use the Message Passing Interface (MPI) as the communication layer and BLAS to perform the local matrix operations. The API provides a friendly interface to the users, hiding almost all the technical aspects related to the parallel execution of the code and the use of the secondary memory to solve the systems. In particular, the API can automatically select the best way to store and solve the systems, depending of the dimension of the system, the number of processes and the main memory of the platform. Experimental results on several parallel platforms report high performance, reaching more than 1 TFLOP with 64 cores to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors. New version program summaryProgram title: Huge Dense System Solver (HDSS) Catalogue identifier: AEHU_v1_1 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEHU_v1_1.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 87 062 No. of bytes in distributed program, including test data, etc.: 1 069 110 Distribution format: tar.gz Programming language: Fortran90, C Computer: Parallel architectures: multiprocessors, computer clusters Operating system: Linux/Unix Has the code been vectorized or parallelized?: Yes, includes MPI primitives. RAM: Tested for up to 190 GB Classification: 6.5 External routines: MPI ( http://www.mpi-forum.org/), BLAS ( http://www.netlib.org/blas/), PLAPACK ( http://www.cs.utexas.edu/~plapack/), POOCLAPACK ( ftp://ftp.cs.utexas.edu/pub/rvdg/PLAPACK/pooclapack.ps) (code for PLAPACK and POOCLAPACK is included in the distribution). Catalogue identifier of previous version: AEHU_v1_0 Journal reference of previous version: Comput. Phys. Comm. 182 (2011) 533 Does the new version supersede the previous version?: Yes Nature of problem: Huge scale dense systems of linear equations, Ax=B, beyond standard LAPACK capabilities. Solution method: The linear systems are solved by means of parallelized routines based on the LU factorization, using efficient secondary storage algorithms when the available main memory is insufficient. Reasons for new version: In many applications we need to guarantee a high accuracy in the solution of very large linear systems and we can do it by using double-precision arithmetic. Summary of revisions: Version 1.1 Can be used to solve linear systems using double-precision arithmetic. New version of the initialization routine. The user can choose the kind of arithmetic and the values of several parameters of the environment. Running time: About 5 hours to solve a system with more than 200 000 equations and more than 10 000 right-hand side vectors using double-precision arithmetic on an eight-node commodity cluster with a total of 64 Intel cores.

The putative serine protease inhibitor Api m 6 from Apis mellifera venom: recombinant and structural evaluation.

PubMed

Michel, Y; McIntyre, M; Ginglinger, H; Ollert, M; Cifuentes, L; Blank, S; Spillner, E

2012-01-01

Immunoglobulin (Ig) E-mediated reactions to honeybee venom can cause severe anaphylaxis, sometimes with fatal consequences. Detailed knowledge of the allergic potential of all venom components is necessary to ensure proper diagnosis and treatment of allergy and to gain a better understanding of the allergological mechanisms of insect venoms. Our objective was to undertake an immunochemical and structural evaluation of the putative low-molecular-weight serine protease inhibitor Api m 6, a component of honeybee venom. We recombinantly produced Api m 6 as a soluble protein in Escherichia coli and in Spodoptera frugiperda (Sf9) insect cells.We also assessed specific IgE reactivity of venom-sensitized patients with 2 prokaryotically produced Api m 6 variants using enzyme-linked immunosorbent assay. Moreover, we built a structural model ofApi m 6 and compared it with other protease inhibitor structures to gain insights into the function of Api m 6. In a population of 31 honeybee venom-allergic patients, 26% showed specific IgE reactivity with prokaryotically produced Api m 6, showing it to be a minor but relevant allergen. Molecular modeling of Api m 6 revealed a typical fold of canonical protease inhibitors, supporting the putative function of this venom allergen. Although Api m 6 has a highly variant surface charge, its epitope distribution appears to be similar to that of related proteins. Api m 6 is a honeybee venom component with IgE-sensitizing potential in a fraction of venom-allergic patients. Recombinant Api m 6 can help elucidate individual component-resolved reactivity profiles and increase our understanding of immune responses to low-molecular-weight allergens

TraceContract

NASA Technical Reports Server (NTRS)

Kavelund, Klaus; Barringer, Howard

2012-01-01

TraceContract is an API (Application Programming Interface) for trace analysis. A trace is a sequence of events, and can, for example, be generated by a running program, instrumented appropriately to generate events. An event can be any data object. An example of a trace is a log file containing events that a programmer has found important to record during a program execution. Trace - Contract takes as input such a trace together with a specification formulated using the API and reports on any violations of the specification, potentially calling code (reactions) to be executed when violations are detected. The software is developed as an internal DSL (Domain Specific Language) in the Scala programming language. Scala is a relatively new programming language that is specifically convenient for defining such internal DSLs due to a number of language characteristics. This includes Scala s elegant combination of object-oriented and functional programming, a succinct notation, and an advanced type system. The DSL offers a combination of data-parameterized state machines and temporal logic, which is novel. As an extension of Scala, it is a very expressive and convenient log file analysis framework.

Continuous manufacturing and analytical characterization of fixed-dose, multilayer orodispersible films.

PubMed

Thabet, Yasmin; Lunter, Dominique; Breitkreutz, Joerg

2018-05-30

Various drug therapies require more than one active pharmaceutical ingredient (API) for an effective treatment. There are many advantages, e.g. to improve the compliance or pharmacodynamic response in comparison to a monotherapy or to increase the therapy safety. Until now, there are only a few products available for the paediatric population due to the lack of age appropriate dosage forms or studies proving the efficacy and safety of these products. This study aims to develop orodispersible films (ODFs) in a continuous solvent casting process as child appropriate dosage form containing both enalapril maleate (EM) and hydrochlorothiazide (HCT) separated in different film layers. Furthermore, they should be characterised and the API migration analysed by confocal Raman microscopy (CRM). ODFs were successfully produced in a continuous manufacturing process in form of double- and triple-layer formulations based on hydroxypropylcellulose (HPC) or a combination of HPC and polyvinyl alcohol (PVA). CRM revealed that both APIs migrate within the film layers shortly after manufacturing. PVA inhibits the migration inside the double-layer film, but is not able to prevent the API migration as an interlayer inside a triple-layer ODF. With increasing film layers, the content of residual solvents and the disintegration time increases (mono-layer films: <10 s, triple-layer films: 37 s). In conclusion, it was feasible to produce fixed-dose combinations in therapeutic doses up to 9 mg HCT and 3.5 mg EM for the double-layer film with adequate mechanical properties, which enable coiling up onto jumbo rolls directly after production. The best separation of the two APIs was achieved by casting a double-layer ODF consisting of different film forming polymers, which can be beneficial when processing two incompatible APIs. Copyright © 2018 Elsevier B.V. All rights reserved.

Surface acidity and solid-state compatibility of excipients with an acid-sensitive API: case study of atorvastatin calcium.

PubMed

Govindarajan, Ramprakash; Landis, Margaret; Hancock, Bruno; Gatlin, Larry A; Suryanarayanan, Raj; Shalaev, Evgenyi Y

2015-04-01

The objectives of this study were to measure the apparent surface acidity of common excipients and to correlate the acidity with the chemical stability of an acid-sensitive active pharmaceutical ingredient (API) in binary API-excipient powder mixtures. The acidity of 26 solid excipients was determined by two methods, (i) by measuring the pH of their suspensions or solutions and (ii) the pH equivalent (pHeq) measured via ionization of probe molecules deposited on the surface of the excipients. The chemical stability of an API, atorvastatin calcium (AC), in mixtures with the excipients was evaluated by monitoring the appearance of an acid-induced degradant, atorvastatin lactone, under accelerated storage conditions. The extent of lactone formation in AC-excipient mixtures was presented as a function of either solution/suspension pH or pHeq. No lactone formation was observed in mixtures with excipients having pHeq > 6, while the lactone levels were pronounced (> 0.6% after 6 weeks at 50°C/20% RH) with excipients exhibiting pHeq < 3. The three pHeq regions (> 6, 3-6, and < 3) were consistent with the reported solution pH-stability profile of AC. In contrast to the pHeq scale, lactone formation did not show any clear trend when plotted as a function of the suspension/solution pH. Two mechanisms to explain the discrepancy between the suspension/solution pH and the chemical stability data were discussed. Acidic excipients, which are expected to be incompatible with an acid-sensitive API, were identified based on pHeq measurements. The incompatibility prediction was confirmed in the chemical stability tests using AC as an example of an acid-sensitive API.

Tenofovir disoproxil fumarate in Asian or Pacific Islander chronic hepatitis B patients with high viral load (≥ 9 log10 copies/ml).

PubMed

Fung, Scott; Gordon, Stuart C; Krastev, Zahary; Horban, Andrzej; Petersen, Jörg; Sperl, Jan; Gane, Edward; Jacobson, Ira M; Yee, Leland J; Dinh, Phillip; Martins, Eduardo B; Flaherty, John F; Kitrinos, Kathryn M; Dusheiko, Geoffrey; Trinh, Huy; Flisiak, Robert; Rustgi, Vinod K; Buti, Maria; Marcellin, Patrick

2015-02-01

We evaluated the antiviral response of Asian or Pacific Islander (API) patients with chronic hepatitis B (CHB) who had baseline high viral load (HVL), defined as pre-treatment hepatitis B virus (HBV) DNA ≥9 log10 copies/ml, following up to 288 weeks of tenofovir disoproxil fumarate (TDF) treatment. A total of 205 HBeAg-negative and HBeAg-positive self-described API patients received 48 weeks of TDF 300 mg (HVL n = 18) or adefovir dipivoxil 10 mg (HVL n = 15) in a blinded fashion, followed by open-label TDF for an additional 240 weeks. The proportions of HVL vs. non-HVL patients with HBV DNA <400 copies/ml were compared. Mean declines in HBV DNA were evaluated in API vs. non-API patients. Throughout the first 72 weeks of treatment, a smaller proportion of HVL API patients reached HBV DNA <400 copies/ml than non-HVL API patients. However, after this timepoint similar proportions of HVL and non-HVL API patients achieved HBV DNA <400 copies/ml (100% vs. 97%, respectively), which was maintained through week 288, where 92% of HVL patients and 99% of non-HVL API patients on treatment had HBV DNA <400 copies/ml. During the 288 weeks of treatment, API patients had similar mean HBV DNA declines as non-API patients, regardless of whether patients were HVL or non-HVL. No API HVL patient had persistent viremia at week 288. No resistance was detected among HVL or non-HVL patients. API patients with HVL CHB achieve HBV DNA <400 copies/ml with long-term TDF treatment; however, achieving viral suppression may take longer for HVL patients relative to non-HVL API patients. © 2014 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

DIRAC in Large Particle Physics Experiments

NASA Astrophysics Data System (ADS)

Stagni, F.; Tsaregorodtsev, A.; Arrabito, L.; Sailer, A.; Hara, T.; Zhang, X.; Consortium, DIRAC

2017-10-01

The DIRAC project is developing interware to build and operate distributed computing systems. It provides a development framework and a rich set of services for both Workload and Data Management tasks of large scientific communities. A number of High Energy Physics and Astrophysics collaborations have adopted DIRAC as the base for their computing models. DIRAC was initially developed for the LHCb experiment at LHC, CERN. Later, the Belle II, BES III and CTA experiments as well as the linear collider detector collaborations started using DIRAC for their computing systems. Some of the experiments built their DIRAC-based systems from scratch, others migrated from previous solutions, ad-hoc or based on different middlewares. Adaptation of DIRAC for a particular experiment was enabled through the creation of extensions to meet their specific requirements. Each experiment has a heterogeneous set of computing and storage resources at their disposal that were aggregated through DIRAC into a coherent pool. Users from different experiments can interact with the system in different ways depending on their specific tasks, expertise level and previous experience using command line tools, python APIs or Web Portals. In this contribution we will summarize the experience of using DIRAC in particle physics collaborations. The problems of migration to DIRAC from previous systems and their solutions will be presented. An overview of specific DIRAC extensions will be given. We hope that this review will be useful for experiments considering an update, or for those designing their computing models.

Perl Embedded in PTC's Pro/ENGINEER, Version 1

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

2003-12-22

Pro-PERL (AKA Pro/PERL) is a Perl extension to the PTC Pro/TOOLKIT API to the PTC Pro/ENGINEER CAD application including an embedded interpreter. It can be used to automate and customize Pro/ENGINEER, create Vendor Neutral Archive (VNA) format files and re-create CAD models from the VNA files. This has applications in sanitizing classified CAD models created in a classified environment for transfer to an open environment, creating template models for modification to finished models by non-expert users, and transfer of design intent data to other modeling technologies.

jqcML: an open-source java API for mass spectrometry quality control data in the qcML format.

PubMed

Bittremieux, Wout; Kelchtermans, Pieter; Valkenborg, Dirk; Martens, Lennart; Laukens, Kris

2014-07-03

The awareness that systematic quality control is an essential factor to enable the growth of proteomics into a mature analytical discipline has increased over the past few years. To this aim, a controlled vocabulary and document structure have recently been proposed by Walzer et al. to store and disseminate quality-control metrics for mass-spectrometry-based proteomics experiments, called qcML. To facilitate the adoption of this standardized quality control routine, we introduce jqcML, a Java application programming interface (API) for the qcML data format. First, jqcML provides a complete object model to represent qcML data. Second, jqcML provides the ability to read, write, and work in a uniform manner with qcML data from different sources, including the XML-based qcML file format and the relational database qcDB. Interaction with the XML-based file format is obtained through the Java Architecture for XML Binding (JAXB), while generic database functionality is obtained by the Java Persistence API (JPA). jqcML is released as open-source software under the permissive Apache 2.0 license and can be downloaded from https://bitbucket.org/proteinspector/jqcml .

75 FR 58014 - Pipeline Safety: Information Collection Activity; Request for Comments

Federal Register 2010, 2011, 2012, 2013, 2014

2010-09-23

... detection systems must comply with the standards set out in American Petroleum Institute (API) publication API 1130. API 1130 requires operators to record and retain certain information regarding the operation and testing of CPM systems. Compliance with API 1130, including its recordkeeping requirements...

Regional framework, structural and petroleum aspects of rift basins in Niger, Chad and the Central African Republic (C.A.R.)

NASA Astrophysics Data System (ADS)

Genik, G. J.

1992-10-01

This paper overviews the regional framework, tectonic, structural and petroleum aspects of rifts in Niger, Chad and the C.A.R. The data base is from mainly proprietary exploration work consisting of some 50,000 kilometres of seismic profiles, 50 exploration wells, one million square kilometres of aeromagnetics coverage and extensive gravity surveys. There have been 13 oil and two oil and gas discoveries. A five phased tectonic history dating from the Pan African orogeny (750-550 MY B.P.) to the present suggests that the Western Central African Rift System (WCAS) with its component West African Rift Subsystem (WAS) and Central African Subsystem (CAS) formed mainly by the mechanical separation of African crustal blocks during the Early Cretaceous. Among the resulting rift basins in Niger, Chad and the C.A.R., seven are in the WAS—Grein, Kafra, Tenere. Tefidet, Termit, Bongor, and N'Dgel Edgi and three, Doba, Doseo, and Salamat are in the CAS. The WAS basins in Niger and Chad are all extensional and contain more than 14,000 m of continental to marine Early Cretaceous to Recent clastic sediments and minor amounts of volcanics. Medium to light oil (20° API-46° API) and gas have been discovered in the Termit basin in reservoir, source and seal beds of Late Cretaceous and Palaeogene age. The most common structural styles are extensional normal fault blocks and transtensional synthetic and antithetic normal fault blocks. The CAS Doba, Doseo and Salamat are extensional to transtensional rift basins containing up to 7500 m of terrestrial mainly Early Cretaceous clastics. Heavy to light oil (15°-39° API) and gas have been discovered in Doba and Doseo basins. Source rocks are Early Cretaceous lacustrine shales, whereas reservoirs and seals are both Early and Late Cretaceous. Dominant structural styles are extensional and transtensional fault blocks, transpressional anticlines and flower structures. The existence of a total rift basin sediment volume of more than one million cubic kilometres with structured reservoir, source and seal rocks favours the generation, migration and entrapment of additional significant volumes of hydrocarbons in many of these basins.

Commercial Building Energy Saver, Web App

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

Hong, Tianzhen; Piette, Mary; Lee, Sang Hoon

The CBES App is a web-based toolkit for use by small businesses and building owners and operators of small and medium size commercial buildings to perform energy benchmarking and retrofit analysis for buildings. The CBES App analyzes the energy performance of user's building for pre-and posto-retrofit, in conjunction with user's input data, to identify recommended retrofit measures, energy savings and economic analysis for the selected measures. The CBES App provides energy benchmarking, including getting an EnergyStar score using EnergyStar API and benchmarking against California peer buildings using the EnergyIQ API. The retrofit analysis includes a preliminary analysis by looking upmore » retrofit measures from a pre-simulated database DEEP, and a detailed analysis creating and running EnergyPlus models to calculate energy savings of retrofit measures. The CBES App builds upon the LBNL CBES API.« less

Formal Analysis of Key Integrity in PKCS#11

NASA Astrophysics Data System (ADS)

Falcone, Andrea; Focardi, Riccardo

PKCS#11 is a standard API to cryptographic devices such as smarcards, hardware security modules and usb crypto-tokens. Though widely adopted, this API has been shown to be prone to attacks in which a malicious user gains access to the sensitive keys stored in the devices. In 2008, Delaune, Kremer and Steel proposed a model to formally reason on this kind of attacks. We extend this model to also describe flaws that are based on integrity violations of the stored keys. In particular, we consider scenarios in which a malicious overwriting of keys might fool honest users into using attacker's own keys, while performing sensitive operations. We further enrich the model with a trusted key mechanism ensuring that only controlled, non-tampered keys are used in cryptographic operations, and we show how this modified API prevents the above mentioned key-replacement attacks.

Detecting Runtime Anomalies in AJAX Applications through Trace Analysis

DTIC Science & Technology

2011-08-10

statements by adding the instrumentation to the GWT UI classes, leaving the user code untouched. Some content management frameworks such as Drupal [12...Google web toolkit.” http://code.google.com/webtoolkit/. [12] “Form generation – drupal api.” http://api.drupal.org/api/group/form_api/6. 9

Multi-Robot Systems in Military Domains (Les Systemes Multi-Robots Dans les Domaines Militaires)

DTIC Science & Technology

2008-12-01

to allow him to react quickly to improve his personal safety , it is mandatory to shorten the current very long delay needed for the human operator to...Hard RT tasks 2 OS / API Process monitoring 3 H / API Flexible communication medium 4 H / API Networking capabilities 5 H / API Safety 6 API...also be considered between high level services and legacy systems. 4) This is the one of the basic requirement for CoRoDe. 5) Safety : CRC, Timeouts

Using USNO's API to Obtain Data

NASA Astrophysics Data System (ADS)

Lesniak, Michael V.; Pozniak, Daniel; Punnoose, Tarun

2015-01-01

The U.S. Naval Observatory (USNO) is in the process of modernizing its publicly available web services into APIs (Application Programming Interfaces). Services configured as APIs offer greater flexibility to the user and allow greater usage. Depending on the particular service, users who implement our APIs will receive either a PNG (Portable Network Graphics) image or data in JSON (JavaScript Object Notation) format. This raw data can then be embedded in third-party web sites or in apps.Part of the USNO's mission is to provide astronomical and timing data to government agencies and the general public. To this end, the USNO provides accurate computations of astronomical phenomena such as dates of lunar phases, rise and set times of the Moon and Sun, and lunar and solar eclipse times. Users who navigate to our web site and select one of our 18 services are prompted to complete a web form, specifying parameters such as date, time, location, and object. Many of our services work for years between 1700 and 2100, meaning that past, present, and future events can be computed. Upon form submission, our web server processes the request, computes the data, and outputs it to the user.Over recent years, the use of the web by the general public has vastly changed. In response to this, the USNO is modernizing its web-based data services. This includes making our computed data easier to embed within third-party web sites as well as more easily querying from apps running on tablets and smart phones. To facilitate this, the USNO has begun converting its services into APIs. In addition to the existing web forms for the various services, users are able to make direct URL requests that return either an image or numerical data.To date, four of our web services have been configured to run with APIs. Two are image-producing services: "Apparent Disk of a Solar System Object" and "Day and Night Across the Earth." Two API data services are "Complete Sun and Moon Data for One Day" and "Dates of Primary Phases of the Moon." Instructions for how to use our API services as well as examples of their use can be found on one of our explanatory web pages and will be discussed here.

Genetic variation in natural honeybee populations, Apis mellifera capensis

NASA Astrophysics Data System (ADS)

Hepburn, Randall; Neumann, Peter; Radloff, Sarah E.

2004-09-01

Genetic variation in honeybee, Apis mellifera, populations can be considerably influenced by breeding and commercial introductions, especially in areas with abundant beekeeping. However, in southern Africa apiculture is based on the capture of wild swarms, and queen rearing is virtually absent. Moreover, the introduction of European subspecies constantly failed in the Cape region. We therefore hypothesize a low human impact on genetic variation in populations of Cape honeybees, Apis mellifera capensis. A novel solution to studying genetic variation in honeybee populations based on thelytokous worker reproduction is applied to test this hypothesis. Environmental effects on metrical morphological characters of the phenotype are separated to obtain a genetic residual component. The genetic residuals are then re-calculated as coefficients of genetic variation. Characters measured included hair length on the abdomen, width and length of wax plate, and three wing angles. The data show for the first time that genetic variation in Cape honeybee populations is independent of beekeeping density and probably reflects naturally occurring processes such as gene flow due to topographic and climatic variation on a microscale.

LBMD : a layer-based mesh data structure tailored for generic API infrastructures.

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

Ebeida, Mohamed S.; Knupp, Patrick Michael

2010-11-01

A new mesh data structure is introduced for the purpose of mesh processing in Application Programming Interface (API) infrastructures. This data structure utilizes a reduced mesh representation to increase its ability to handle significantly larger meshes compared to full mesh representation. In spite of the reduced representation, each mesh entity (vertex, edge, face, and region) is represented using a unique handle, with no extra storage cost, which is a crucial requirement in most API libraries. The concept of mesh layers makes the data structure more flexible for mesh generation and mesh modification operations. This flexibility can have a favorable impactmore » in solver based queries of finite volume and multigrid methods. The capabilities of LBMD make it even more attractive for parallel implementations using Message Passing Interface (MPI) or Graphics Processing Units (GPUs). The data structure is associated with a new classification method to relate mesh entities to their corresponding geometrical entities. The classification technique stores the related information at the node level without introducing any ambiguities. Several examples are presented to illustrate the strength of this new data structure.« less

Diagnosis and treatment of limb fractures associated with acute peripheral ischemia.

PubMed

Popescu, G I; Lupescu, O; Nagea, M; Patru, C

2013-01-01

Acute Peripheral Ischemia (API) is the most severe acute complication after both open and closed fractures, as ischemia compromises not only the vitality of the affected limb, but also the patient's life, because metabolic anaerobic changes following ischemia have serious local and general consequences. These explain why early diagnosis of API is very important for the prognosis of the traumatized limb.The authors analyse cases when API was not diagnosed immediately after trauma, but some time after the first examination, due to either low systolic BP or to late onset of API. The patients were analysed concerning the type of the fracture, the reason for delayed diagnosis of API, the moment of API diagnosis and the arterial injury. In all those cases, surgery was performed immediately after API diagnosis, in order to identify and treat the complex injuries(bone and vascular). Celsius.

Extending the XNAT archive tool for image and analysis management in ophthalmology research

NASA Astrophysics Data System (ADS)

Wahle, Andreas; Lee, Kyungmoo; Harding, Adam T.; Garvin, Mona K.; Niemeijer, Meindert; Sonka, Milan; Abràmoff, Michael D.

2013-03-01

In ophthalmology, various modalities and tests are utilized to obtain vital information on the eye's structure and function. For example, optical coherence tomography (OCT) is utilized to diagnose, screen, and aid treatment of eye diseases like macular degeneration or glaucoma. Such data are complemented by photographic retinal fundus images and functional tests on the visual field. DICOM isn't widely used yet, though, and frequently images are encoded in proprietary formats. The eXtensible Neuroimaging Archive Tool (XNAT) is an open-source NIH-funded framework for research PACS and is in use at the University of Iowa for neurological research applications. Its use for ophthalmology was hence desirable but posed new challenges due to data types thus far not considered and the lack of standardized formats. We developed custom tools for data types not natively recognized by XNAT itself using XNAT's low-level REST API. Vendor-provided tools can be included as necessary to convert proprietary data sets into valid DICOM. Clients can access the data in a standardized format while still retaining the original format if needed by specific analysis tools. With respective project-specific permissions, results like segmentations or quantitative evaluations can be stored as additional resources to previously uploaded datasets. Applications can use our abstract-level Python or C/C++ API to communicate with the XNAT instance. This paper describes concepts and details of the designed upload script templates, which can be customized to the needs of specific projects, and the novel client-side communication API which allows integration into new or existing research applications.

Infectivity and virulence of Nosema ceranae and Nosema apis in commercially available North American honey bees

USDA-ARS?s Scientific Manuscript database

Nosema ceranae infection is ubiquitous in western honey bees, Apis mellifera. In the US, displacement of N. apis in bee colonies suggests that N. ceranae has competitive advantages. Our study, however, showed that N. ceranae was significantly less infective and less virulent than N. apis in commerc...

47 CFR 61.46 - Adjustments to the API.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 47 Telecommunication 3 2014-10-01 2014-10-01 false Adjustments to the API. 61.46 Section 61.46... Rules for Dominant Carriers § 61.46 Adjustments to the API. (a) Except as provided in paragraphs (d) and... cap local exchange carrier must calculate an API for each affected basket pursuant to the following...

47 CFR 61.46 - Adjustments to the API.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 47 Telecommunication 3 2012-10-01 2012-10-01 false Adjustments to the API. 61.46 Section 61.46... Rules for Dominant Carriers § 61.46 Adjustments to the API. (a) Except as provided in paragraphs (d) and... cap local exchange carrier must calculate an API for each affected basket pursuant to the following...

47 CFR 61.46 - Adjustments to the API.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 47 Telecommunication 3 2011-10-01 2011-10-01 false Adjustments to the API. 61.46 Section 61.46... Rules for Dominant Carriers § 61.46 Adjustments to the API. (a) Except as provided in paragraphs (d) and... cap local exchange carrier must calculate an API for each affected basket pursuant to the following...

47 CFR 61.46 - Adjustments to the API.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 47 Telecommunication 3 2010-10-01 2010-10-01 false Adjustments to the API. 61.46 Section 61.46... Rules for Dominant Carriers § 61.46 Adjustments to the API. (a) Except as provided in paragraphs (d) and... carrier must calculate an API for each affected basket pursuant to the following methodology: APIt = APIt...

47 CFR 61.46 - Adjustments to the API.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 47 Telecommunication 3 2013-10-01 2013-10-01 false Adjustments to the API. 61.46 Section 61.46... Rules for Dominant Carriers § 61.46 Adjustments to the API. (a) Except as provided in paragraphs (d) and... cap local exchange carrier must calculate an API for each affected basket pursuant to the following...

Compositional mining of multiple object API protocols through state abstraction.

PubMed

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

2013-01-01

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

Compositional Mining of Multiple Object API Protocols through State Abstraction

PubMed Central

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

2013-01-01

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

Experimental cocrystal screening and solution based scale-up cocrystallization methods.

PubMed

Malamatari, Maria; Ross, Steven A; Douroumis, Dennis; Velaga, Sitaram P

2017-08-01

Cocrystals are crystalline single phase materials composed of two or more different molecular and/or ionic compounds generally in a stoichiometric ratio which are neither solvates nor simple salts. If one of the components is an active pharmaceutical ingredient (API), the term pharmaceutical cocrystal is often used. There is a growing interest among drug development scientists in exploring cocrystals, as means to address physicochemical, biopharmaceutical and mechanical properties and expand solid form diversity of the API. Conventionally, coformers are selected based on crystal engineering principles, and the equimolar mixtures of API and coformers are subjected to solution-based crystallization that are commonly employed in polymorph and salt screening. However, the availability of new knowledge on cocrystal phase behaviour in solid state and solutions has spurred the development and implementation of more rational experimental cocrystal screening as well as scale-up methods. This review aims to provide overview of commonly employed solid form screening techniques in drug development with an emphasis on cocrystal screening methodologies. The latest developments in understanding and the use of cocrystal phase diagrams in both screening and solution based scale-up methods are also presented. Final section is devoted to reviewing the state of the art research covering solution based scale-up cocrystallization process for different cocrystals besides more recent continuous crystallization methods. Copyright © 2017 Elsevier B.V. All rights reserved.

Near infrared and Raman spectroscopy as Process Analytical Technology tools for the manufacturing of silicone-based drug reservoirs.

PubMed

Mantanus, J; Rozet, E; Van Butsele, K; De Bleye, C; Ceccato, A; Evrard, B; Hubert, Ph; Ziémons, E

2011-08-05

Using near infrared (NIR) and Raman spectroscopy as PAT tools, 3 critical quality attributes of a silicone-based drug reservoir were studied. First, the Active Pharmaceutical Ingredient (API) homogeneity in the reservoir was evaluated using Raman spectroscopy (mapping): the API distribution within the industrial drug reservoirs was found to be homogeneous while API aggregates were detected in laboratory scale samples manufactured with a non optimal mixing process. Second, the crosslinking process of the reservoirs was monitored at different temperatures with NIR spectroscopy. Conformity tests and Principal Component Analysis (PCA) were performed on the collected data to find out the relation between the temperature and the time necessary to reach the crosslinking endpoints. An agreement was found between the conformity test results and the PCA results. Compared to the conformity test method, PCA had the advantage to discriminate the heating effect from the crosslinking effect occurring together during the monitored process. Therefore the 2 approaches were found to be complementary. Third, based on the HPLC reference method, a NIR model able to quantify the API in the drug reservoir was developed and thoroughly validated. Partial Least Squares (PLS) regression on the calibration set was performed to build prediction models of which the ability to quantify accurately was tested with the external validation set. The 1.2% Root Mean Squared Error of Prediction (RMSEP) of the NIR model indicated the global accuracy of the model. The accuracy profile based on tolerance intervals was used to generate a complete validation report. The 95% tolerance interval calculated on the validation results indicated that each future result will have a relative error below ±5% with a probability of at least 95%. In conclusion, 3 critical quality attributes of silicone-based drug reservoirs were quickly and efficiently evaluated by NIR and Raman spectroscopy. Copyright © 2011 Elsevier B.V. All rights reserved.

Mobile Phone Application Development for the Classroom

NASA Astrophysics Data System (ADS)

Lewis, P.; Oostra, D.; Crecelius, S.; Chambers, L. H.

2012-08-01

With smartphone sales currently surpassing laptop sales, it is hard not to think that these devices will have a place in the classroom. More specifically, with little to no monetary investment, classroom-centric mobile applications have the ability to suit the needs of teachers. Previously, programming such an item was a daunting task to the classroom teacher. But now, through the use of online visual tools, anyone has the ability to generate a mobile application to suit individual classroom needs. The "MY NASA DATA" (MND) project has begun work on such an application. Using online tools that are directed at the non-programmer, the team has developed two usable mobile applications ("apps") that fit right into the science classroom. The two apps generated include a cloud dichotomous key for cloud identification in the field, and an atmospheric science glossary to help with standardized testing key vocabulary and classroom assignments. Through the use of free online tools, teachers and students now have the ability to customize mobile applications to meet their individual needs. As an extension of the mobile applications, the MND team is planning web-based application programming interfaces (API's) that will be generated from data that is currently included in the MND Live Access Server. This will allow teachers and students to choose data sets that they want to include in the mobile application without having to populate the API themselves. Through the use of easy to understand online mobile app tutorials and MND data sets, teachers will have the ability to generate unit-specific mobile applications to further engage and empower students in the science classroom.

A fifth major genetic group among honeybees revealed in Syria

PubMed Central

2013-01-01

Background Apiculture has been practiced in North Africa and the Middle-East from antiquity. Several thousand years of selective breeding have left a mosaic of Apis mellifera subspecies in the Middle-East, many uniquely adapted and survived to local environmental conditions. In this study we explore the genetic diversity of A. mellifera from Syria (n = 1258), Lebanon (n = 169) and Iraq (n = 35) based on 14 short tandem repeat (STR) loci in the context of reference populations from throughout the Old World (n = 732). Results Our data suggest that the Syrian honeybee Apis mellifera syriaca occurs in both Syrian and Lebanese territories, with no significant genetic variability between respective populations from Syria and Lebanon. All studied populations clustered within a new fifth independent nuclear cluster, congruent with an mtDNA Z haplotype identified in a previous study. Syrian honeybee populations are not associated with Oriental lineage O, except for sporadic introgression into some populations close to the Turkish and Iraqi borders. Southern Syrian and Lebanese populations demonstrated high levels of genetic diversity compared to the northern populations. Conclusion This study revealed the effects of foreign queen importations on Syrian bee populations, especially for the region of Tartus, where extensive introgression of A. m. anatolica and/or A. m. caucasica alleles were identified. The policy of creating genetic conservation centers for the Syrian subspecies should take into consideration the influence of the oriental lineage O from the northern Syrian border and the large population of genetically divergent indigenous honeybees located in southern Syria. PMID:24314104

A REST-ful interpretation for embedded modular systems based on open architecture

NASA Astrophysics Data System (ADS)

Lyke, James

2016-05-01

The much-anticipated revolution of the "Internet of things" (IoT) is expected to generate one trillion internet devices within the next 15 years, mostly in the form of simple wireless sensor devices. While this revolution promises to transform silicon markets and drive a number of disruptive changes in society, it is also the case that the protocols, complexity, and security issues of extremely large dynamic, co-mingled networks is still poorly understood. Furthermore, embedded system developers, to include military and aerospace users, have largely ignored the potential (good and bound) of the cloudlike, possibly intermingling networks having variable structure to how future systems might be engineered. In this paper, we consider a new interpretation of IoT inspired modular architecture strategies involving the representational state transfer (REST) model, in which dynamic networks with variable structure employ stateless application programming interface (API) concepts. The power of the method, which extends concepts originally developed for space plug-and-play avionics, is that it allows for the fluid co-mingling of hardware and software in networks whose structure can overlap and evolve. Paradoxically, these systems may have the most stringent determinism and fault-tolerant needs. In this paper we review how RESTful APIs can potentially be used to design, create, test, and deploy systems rapidly while addressing security and referential integrity even when the nodes of many systems might physically co-mingle. We will also explore ways to take advantage of the RESTful paradigm for fault tolerance and what extensions might be necessary to deal with high-performance and determinism.

Resolution and sensitivity of the eyes of the Asian honeybees Apis florea, Apis cerana and Apis dorsata.

PubMed

Somanathan, Hema; Warrant, Eric J; Borges, Renee M; Wallén, Rita; Kelber, Almut

2009-08-01

Bees of the genus Apis are important foragers of nectar and pollen resources. Although the European honeybee, Apis mellifera, has been well studied with respect to its sensory abilities, learning behaviour and role as pollinators, much less is known about the other Apis species. We studied the anatomical spatial resolution and absolute sensitivity of the eyes of three sympatric species of Asian honeybees, Apis cerana, Apis florea and Apis dorsata and compared them with the eyes of A. mellifera. Of these four species, the giant honeybee A. dorsata (which forages during moonlit nights) has the lowest spatial resolution and the most sensitive eyes, followed by A. mellifera, A. cerana and the dwarf honeybee, A. florea (which has the smallest acceptance angles and the least sensitive eyes). Moreover, unlike the strictly diurnal A. cerana and A. florea, A. dorsata possess large ocelli, a feature that it shares with all dim-light bees. However, the eyes of the facultatively nocturnal A. dorsata are much less sensitive than those of known obligately nocturnal bees such as Megalopta genalis in Panama and Xylocopa tranquebarica in India. The differences in sensitivity between the eyes of A. dorsata and other strictly diurnal Apis species cannot alone explain why the former is able to fly, orient and forage at half-moon light levels. We assume that additional neuronal adaptations, as has been proposed for A. mellifera, M. genalis and X. tranquebarica, might exist in A. dorsata.

Improving the API dissolution rate during pharmaceutical hot-melt extrusion I: Effect of the API particle size, and the co-rotating, twin-screw extruder screw configuration on the API dissolution rate.

PubMed

Li, Meng; Gogos, Costas G; Ioannidis, Nicolas

2015-01-15

The dissolution rate of the active pharmaceutical ingredients in pharmaceutical hot-melt extrusion is the most critical elementary step during the extrusion of amorphous solid solutions - total dissolution has to be achieved within the short residence time in the extruder. Dissolution and dissolution rates are affected by process, material and equipment variables. In this work, we examine the effect of one of the material variables and one of the equipment variables, namely, the API particle size and extruder screw configuration on the API dissolution rate, in a co-rotating, twin-screw extruder. By rapidly removing the extruder screws from the barrel after achieving a steady state, we collected samples along the length of the extruder screws that were characterized by polarized optical microscopy (POM) and differential scanning calorimetry (DSC) to determine the amount of undissolved API. Analyses of samples indicate that reduction of particle size of the API and appropriate selection of screw design can markedly improve the dissolution rate of the API during extrusion. In addition, angle of repose measurements and light microscopy images show that the reduction of particle size of the API can improve the flowability of the physical mixture feed and the adhesiveness between its components, respectively, through dry coating of the polymer particles by the API particles. Copyright © 2014. Published by Elsevier B.V.

Comparison of Vitek Matrix-assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry Versus Conventional Methods in Candida Identification.

PubMed

Keçeli, Sema Aşkın; Dündar, Devrim; Tamer, Gülden Sönmez

2016-02-01

Candida species are generally identified by conventional methods such as germ tube or morphological appearance on corn meal agar, biochemical methods using API kits and molecular biological methods. Alternative to these methods, rapid and accurate identification methods of microorganisms called matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDİ-TOF MS) has recently been described. In this study, Candida identification results by API Candida kit, API 20C AUX kit and identifications on corn meal agar (CMA) are compared with the results obtained on Vitek-MS. All results were confirmed by sequencing internal transcribed spacer (ITS) regions of rDNA. Totally, 97 Candida strains were identified by germ tube test, CMA, API and Vitek-MS. Vitek-MS results were compatible with 74.2 % of API 20C AUX and 81.4 % of CMA results. The difference between the results of API Candida and API 20C AUX was detected. The ratio of discrepancy between Vitek-MS and API 20C AUX was 25.8 %. Candida species mostly identified as C. famata or C. tropicalis by and not compatible with API kits were identified as C. albicans by Vitek-MS. Sixteen Candida species having discrepant results with Vitek-MS, API or CMA were randomly chosen, and ITS sequence analysis was performed. The results of sequencing were compatible 56.2 % with API 20C AUX, 50 % with CMA and 93.7 % with Vitek-MS. When compared with conventional identification methods, MS results are more reliable and rapid for Candida identification. MS system may be used as routine identification method in clinical microbiology laboratories.

Development of an in-line Raman spectroscopic method for continuous API quantification during twin-screw wet granulation.

PubMed

Harting, Julia; Kleinebudde, Peter

2018-04-01

Raman spectroscopy was evaluated as a process analytical technology (PAT) tool for continuous API quantification during twin-screw wet granulation. Therefore, a Raman probe was implemented in front of the granulator barrel. This setup enabled the collection of Raman spectra upon a constant granule flow. To develop an in-line PLS calibration model, eight binary mixtures of the API and lactose monohydrate with API contents between 5 and 50% were pre-blended and granulated in a twin-screw granulator with a screw speed of 150 rpm and a powder feed rate of 40 g/min. Water was used as a granulation liquid with different liquid to solid ratios depending on the API content. Ibuprofen and diclofenac sodium were chosen as model drugs and separated PLS models were built for each API. The predictive performance of the developed PLS models was determined by granulating and monitoring new test samples containing different API concentrations. This evaluation showed that the models were able to predict the API concentration with an RMSEP of 0.59% for ibuprofen and 1.5% for diclofenac sodium. In a second part, the developed in-line Raman spectroscopic method was used to determine the API concentration during a split feeding process. Therefore, the API and lactose monohydrate were added by two independently adjustable feeders into the twin-screw granulator barrel. The in-line spectroscopy analysis which was verified by UV-analysis indicated that the mixing ability of the twin-screw granulator was good for the used settings and all adjusted API concentrations. Copyright © 2018 Elsevier B.V. All rights reserved.

Ingredientes Farmacéuticos Activos Potencialmente Inapropiados en Adultos Mayores: Lista IFAsPIAM: Panel de Consenso Argentino.

PubMed

Marzi, Marta M; Pires, Miryam S; Quaglia, Nora B

2018-04-18

To perform a list agreed by Argentinean experts and adapted to the local context containing potentially inappropriate (PI) medications in old people (OP) usingthe Delphi consensus technique optimized for this subject. A preliminary list of potentially inappropriate medications (PIM) was drawn up based on foreign PIM lists and a selective search in the scientific literature. The iterative Delphi process was used to submit the active pharmaceutical ingredients (APIs) of the preliminary PIM list to the panel of Argentinean experts. The analysis of theanswers to determine the arrival to the consensus was carried out applying three criteria specially defined for this purpose. After two Delphi rounds, it was not reached agreement about 12 APIs. The List of explicit criteria for PIAPIs for use in OP (IFAsPIAM List) was finally constituted by 128 APIs corresponding to 9 groups of the ATC classification system to which they were organized. In addition to each API, information justifying the unfavorable benefit/risk profile and therapeutic alternatives or recommendations/precautions was recorded. The group with the most PI APIs was N (NervousSystem) (60; 47%) followed by groups C (Cardiovascular) and M (Musculoskeletal). This study presents the first Latin American list of PIM in OP developed using an expert consensus technique. The IFAs PIAM List would contribute to the rational use of drugs in elderly population, constituting a valuable tool in Argentinean public health. Copyright © 2018. Published by Elsevier Inc.

A commercial project for private investments. Update of the 280 MW api Energia IGCC plant construction in central Italy.

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

Del Bravo, R.; Pinacci, P.; Trifilo, R.

1998-07-01

This paper has the aim to give a general overview of the api Energia IGCC project starting from the project background in 1992 and ending with the progress of construction. api Energia S.p.A., a joint VENTURE between api anonima petroli italiana S.p.A., Roma, Italy (51%), ABB Sae Sadelmi S.p.A., Milano, Italy (25%) and Texaco Development Corporation (24%), is building a 280 MW Integrated Gasification Combined Cycle plant in the api refinery at Falconara Marittima, on Italy' s Adriatic coast, using heavy oil residues. The plant is based on the modern concept of employing a highly efficient combined cycle power plantmore » fed with a low heating value fuel gas produced by gasifying heavy refinery residues. This scheme provides consistent advantages in terms of efficiency and environmental impact over alternative applications of the refinery residues. The electric power produced will feed the national grid. The project has been financed using the ``project financing'' scheme: over 1,000 billion Lira, representing 75% of the overall capital requirement, have been provided by a pool of international banks. In November 1996 the project reached financial closure and immediately after the detailed design and procurement activities started. Engineering, Procurement and Construction activities, carried out by a Consortium of companies of the ABB group, are totally in line with the schedule. Commercial operation of the plant, is scheduled for November 1999.« less

A New Metazoan Recombination Rate Record and Consistently High Recombination Rates in the Honey Bee Genus Apis Accompanied by Frequent Inversions but Not Translocations.

PubMed

Rueppell, Olav; Kuster, Ryan; Miller, Katelyn; Fouks, Bertrand; Rubio Correa, Sara; Collazo, Juan; Phaincharoen, Mananya; Tingek, Salim; Koeniger, Nikolaus

2016-12-01

Western honey bees (Apis mellifera) far exceed the commonly observed 1–2 meiotic recombination events per chromosome and exhibit the highest Metazoan recombination rate (20 cM/Mb) described thus far. However, the reasons for this exceptional rate of recombination are not sufficiently understood. In a comparative study, we report on the newly constructed genomic linkage maps of Apis florea and Apis dorsata that represent the two honey bee lineages without recombination rate estimates so far. Each linkage map was generated de novo, based on SNP genotypes of haploid male offspring of a single female. The A. florea map spans 4,782 cM with 1,279 markers in 16 linkage groups. The A. dorsata map is 5,762 cM long and contains 1,189 markers in 16 linkage groups. Respectively, these map sizes result in average recombination rate estimates of 20.8 and 25.1 cM/Mb. Synteny analyses indicate that frequent intra-chromosomal rearrangements but no translocations among chromosomes accompany the high rates of recombination during the independent evolution of the three major honey bee lineages. Our results imply a common cause for the evolution of very high recombination rates in Apis. Our findings also suggest that frequent homologous recombination during meiosis might increase ectopic recombination and rearrangements within but not between chromosomes. It remains to be investigated whether the resulting inversions may have been important in the evolutionary differentiation between honey bee species.

Sodium alginate: A promising biopolymer for corrosion protection of API X60 high strength carbon steel in saline medium.

PubMed

Obot, I B; Onyeachu, Ikenna B; Kumar, A Madhan

2017-12-15

Sodium alginate (SA), a polysaccharide biopolymer, has been studied as an effective inhibitor against the corrosion of API X60 steel in neutral 3.5% NaCl using gravimetric and electrochemical techniques (OCP, EIS and EFM). The inhibition efficiency of the SA increased with concentration but was lower at higher temperature (70°C). Electrochemical measurements showed that the SA shifted the steel corrosion potential to more positive value and reduced the kinetics of corrosion by forming an adsorbed layer which mitigated the steel surface wetting, based on contact angle measurement. SEM-EDAX was used to confirm the inhibition of SA on API X60 steel surfaces. The SA adsorbs on the steel surface through a physisorption mechanism using its carboxylate oxygen according to UV-vis and ATR-IR measurements, respectively. This phenomena result in decreased localized pitting corrosion of the API X60 steel in 3.5% NaCl solution. Theoretical results using quantum chemical calculations and Monte Carlo simulations provide further atomic level insights into the interaction of SA with steel surface. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Value of Pre-Screening in the Alzheimer's Prevention Initiative (API) Autosomal Dominant Alzheimer's Disease Trial.

PubMed

Rios-Romenets, S; Giraldo-Chica, M; López, H; Piedrahita, F; Ramos, C; Acosta-Baena, N; Muñoz, C; Ospina, P; Tobón, C; Cho, W; Ward, M; Langbaum, J B; Tariot, P N; Reiman, E M; Lopera, F

2018-01-01

The Alzheimer's Prevention Initiative (API) Autosomal Dominant Alzheimer's Disease (ADAD) trial evaluates the anti-amyloid-β antibody crenezumab in cognitively unimpaired persons who, based on genetic background and age, are at high imminent risk of clinical progression, and provides a powerful test of the amyloid hypothesis. The Neurosciences Group of Antioquia implemented a pre-screening process with the goals of decreasing screen failures and identifying participants most likely to adhere to trial requirements of the API ADAD trial in cognitively unimpaired members of Presenilin1 E280A mutation kindreds. The pre-screening failure rate was 48.2%: the primary reason was expected inability to comply with the protocol, chiefly due to work requirements. More carriers compared to non-carriers, and more males compared to females, failed pre-screening. Carriers with illiteracy or learning/comprehension difficulties failed pre-screening more than non-carriers. With the Colombian API Registry and our prescreening efforts, we randomized 169 30-60 year-old cognitively unimpaired carriers and 83 non-carriers who agreed to participate in the trial for at least 60 months. Our findings suggest multiple benefits of implementing a pre-screening process for enrolling prevention trials in ADAD.

Long-Term Temporal Trends of Nosema spp. Infection Prevalence in Northeast Germany: Continuous Spread of Nosema ceranae, an Emerging Pathogen of Honey Bees (Apis mellifera), but No General Replacement of Nosema apis.

PubMed

Gisder, Sebastian; Schüler, Vivian; Horchler, Lennart L; Groth, Detlef; Genersch, Elke

2017-01-01

The Western honey bee ( Apis mellifera ) is widely used as commercial pollinator in worldwide agriculture and, therefore, plays an important role in global food security. Among the parasites and pathogens threatening health and survival of honey bees are two species of microsporidia, Nosema apis and Nosema ceranae. Nosema ceranae is considered an emerging pathogen of the Western honey bee. Reports on the spread of N. ceranae suggested that this presumably highly virulent species is replacing its more benign congener N. apis in the global A. mellifera population. We here present a 12 year longitudinal cohort study on the prevalence of N. apis and N. ceranae in Northeast Germany. Between 2005 and 2016, a cohort of about 230 honey bee colonies originating from 23 apiaries was sampled twice a year (spring and autumn) resulting in a total of 5,600 bee samples which were subjected to microscopic and molecular analysis for determining the presence of infections with N. apis or/and N. ceranae . Throughout the entire study period, both N. apis - and N. ceranae -infections could be diagnosed within the cohort. Logistic regression analysis of the prevalence data demonstrated a significant increase of N. ceranae -infections over the last 12 years, both in autumn (reflecting the development during the summer) and in spring (reflecting the development over winter) samples. Cell culture experiments confirmed that N. ceranae has a higher proliferative potential than N. apis at 27° and 33°C potentially explaining the increase in N. ceranae prevalence during summer. In autumn, characterized by generally low infection prevalence, this increase was accompanied by a significant decrease in N. apis -infection prevalence. In contrast, in spring, the season with a higher prevalence of infection, no significant decrease of N. apis infections despite a significant increase in N. ceranae infections could be observed. Therefore, our data do not support a general advantage of N. ceranae over N. apis and an overall replacement of N. apis by N. ceranae in the studied honey bee population.

Long-Term Temporal Trends of Nosema spp. Infection Prevalence in Northeast Germany: Continuous Spread of Nosema ceranae, an Emerging Pathogen of Honey Bees (Apis mellifera), but No General Replacement of Nosema apis

PubMed Central

Gisder, Sebastian; Schüler, Vivian; Horchler, Lennart L.; Groth, Detlef; Genersch, Elke

2017-01-01

The Western honey bee (Apis mellifera) is widely used as commercial pollinator in worldwide agriculture and, therefore, plays an important role in global food security. Among the parasites and pathogens threatening health and survival of honey bees are two species of microsporidia, Nosema apis and Nosema ceranae. Nosema ceranae is considered an emerging pathogen of the Western honey bee. Reports on the spread of N. ceranae suggested that this presumably highly virulent species is replacing its more benign congener N. apis in the global A. mellifera population. We here present a 12 year longitudinal cohort study on the prevalence of N. apis and N. ceranae in Northeast Germany. Between 2005 and 2016, a cohort of about 230 honey bee colonies originating from 23 apiaries was sampled twice a year (spring and autumn) resulting in a total of 5,600 bee samples which were subjected to microscopic and molecular analysis for determining the presence of infections with N. apis or/and N. ceranae. Throughout the entire study period, both N. apis- and N. ceranae-infections could be diagnosed within the cohort. Logistic regression analysis of the prevalence data demonstrated a significant increase of N. ceranae-infections over the last 12 years, both in autumn (reflecting the development during the summer) and in spring (reflecting the development over winter) samples. Cell culture experiments confirmed that N. ceranae has a higher proliferative potential than N. apis at 27° and 33°C potentially explaining the increase in N. ceranae prevalence during summer. In autumn, characterized by generally low infection prevalence, this increase was accompanied by a significant decrease in N. apis-infection prevalence. In contrast, in spring, the season with a higher prevalence of infection, no significant decrease of N. apis infections despite a significant increase in N. ceranae infections could be observed. Therefore, our data do not support a general advantage of N. ceranae over N. apis and an overall replacement of N. apis by N. ceranae in the studied honey bee population. PMID:28730143

Limitations of high dose carrier based formulations.

PubMed

Yeung, Stewart; Traini, Daniela; Tweedie, Alan; Lewis, David; Church, Tanya; Young, Paul M

2018-06-10

This study was performed to investigate how increasing the active pharmaceutical ingredient (API) content within a formulation affects the dispersion of particles and the aerosol performance efficiency of a carrier based dry powder inhalable (DPI) formulation, using a custom dry powder inhaler (DPI) development rig. Five formulations with varying concentrations of API beclomethasone dipropionate (BDP) between 1% and 30% (w/w) were formulated as a multi-component carrier system containing coarse lactose and fine lactose with magnesium stearate. The morphology of the formulation and each component were investigated using scanning electron micrographs while the particle size was measured by laser diffraction. The aerosol performance, in terms of aerodynamic diameter, was assessed using the British pharmacopeia Apparatus E cascade impactor (Next generation impactor). Chemical analysis of the API was observed by high performance liquid chromatography (HPLC). Increasing the concentration of BDP in the blend resulted in increasing numbers and size of individual agglomerates and densely packed BDP multi-layers on the surface of the lactose carrier. BDP present within the multi-layer did not disperse as individual primary particles but as dense agglomerates, which led to a decrease in aerosol performance and increased percentage of BDP deposition within the Apparatus E induction port and pre-separator. As the BDP concentration in the blends increases, aerosol performance of the formulation decreases, in an inversely proportional manner. Concurrently, the percentage of API deposition in the induction port and pre-separator could also be linked to the amount of micronized particles (BDP and Micronized composite carrier) present in the formulation. The effect of such dose increase on the behaviour of aerosol dispersion was investigated to gain greater insight in the development and optimisation of higher dosed carrier-based formulations. Copyright © 2018 Elsevier B.V. All rights reserved.

Active peptidomimetic insect kinin analogs with type VI turn motif 4-aminopyroglutamate lack native peptide bonds

USDA-ARS?s Scientific Manuscript database

Two stereochemical variant insect kinin mimetic analogs 1796 and 1797 containing (2S,4S)-APy (APy) and (2R,4S)-APy (Apy), respectively, were synthesized and evaluated on isolated Malpighian tubules of the house cricket Acheta domesticus to determine if they could retain the fluid secretion stimulat...

Provenance Store Evaluation

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

Paulson, Patrick R.; Gibson, Tara D.; Schuchardt, Karen L.

2008-03-01

Requirements for the provenance store and access API are developed. Existing RDF stores and APIs are evaluated against the requirements and performance benchmarks. The team’s conclusion is to use MySQL as a database backend, with a possible move to Oracle in the near-term future. Both Jena and Sesame’s APIs will be supported, but new code will use the Jena API

A Monte Carlo modeling alternative for the API Gamma Ray Calibration Facility.

PubMed

Galford, J E

2017-04-01

The gamma ray pit at the API Calibration Facility, located on the University of Houston campus, defines the API unit for natural gamma ray logs used throughout the petroleum logging industry. Future use of the facility is uncertain. An alternative method is proposed to preserve the gamma ray API unit definition as an industry standard by using Monte Carlo modeling to obtain accurate counting rate-to-API unit conversion factors for gross-counting and spectral gamma ray tool designs. Copyright © 2017 Elsevier Ltd. All rights reserved.

Investigation of Dissolution Behavior HPMC/Eudragit®/Magnesium Aluminometasilicate Oral Matrices Based on NMR Solid-State Spectroscopy and Dynamic Characteristics of Gel Layer.

PubMed

Naiserová, M; Kubová, K; Vysloužil, J; Pavloková, S; Vetchý, D; Urbanová, M; Brus, J; Vysloužil, J; Kulich, P

2018-02-01

Burst drug release is often considered a negative phenomenon resulting in unexpected toxicity or tissue irritation. Optimal release of a highly soluble active pharmaceutical ingredient (API) from hypromellose (HPMC) matrices is technologically impossible; therefore, a combination of polymers is required for burst effect reduction. Promising variant could be seen in combination of HPMC and insoluble Eudragits ® as water dispersions. These can be applied only on API/insoluble filler mixture as over-wetting prevention. The main hurdle is a limited water absorption capacity (WAC) of filler. Therefore, the object of this study was to investigate the dissolution behavior of levetiracetam from HPMC/Eudragit ® NE matrices using magnesium aluminometasilicate (Neusilin ® US2) as filler with excellent WAC. Part of this study was also to assess influence of thermal treatment on quality parameters of matrices. The use of Neusilin ® allowed the application of Eudragit ® dispersion to API/Neusilin ® mixture in one step during high-shear wet granulation. HPMC was added extragranularly. Obtained matrices were investigated for qualitative characteristics, NMR solid-state spectroscopy (ssNMR), gel layer dynamic parameters, SEM, and principal component analysis (PCA). Decrease in burst effect (max. of 33.6%) and dissolution rate, increase in fitting to zero-order kinetics, and paradoxical reduction in gel layer thickness were observed with rising Eudragit ® NE concentration. The explanation was done by ssNMR, which clearly showed a significant reduction of the API particle size (150-500 nm) in granules as effect of surfactant present in dispersion in dependence on Eudragit ® NE amount. This change in API particle size resulted in a significantly larger interface between these two entities. Based on ANOVA and PCA, thermal treatment was not revealed as a useful procedure for this system.

A Mathematical Model of Intra-Colony Spread of American Foulbrood in European Honeybees (Apis mellifera L.).

PubMed

Jatulan, Eduardo O; Rabajante, Jomar F; Banaay, Charina Gracia B; Fajardo, Alejandro C; Jose, Editha C

2015-01-01

American foulbrood (AFB) is one of the severe infectious diseases of European honeybees (Apis mellifera L.) and other Apis species. This disease is caused by a gram-positive, spore-forming bacterium Paenibacillus larvae. In this paper, a compartmental (SI framework) model is constructed to represent the spread of AFB within a colony. The model is analyzed to determine the long-term fate of the colony once exposed to AFB spores. It was found out that without effective and efficient treatment, AFB infection eventually leads to colony collapse. Furthermore, infection thresholds were predicted based on the stability of the equilibrium states. The number of infected cell combs is one of the factors that drive disease spread. Our results can be used to forecast the transmission timeline of AFB infection and to evaluate the control strategies for minimizing a possible epidemic.

Fluxes of 13 selected pharmaceuticals in the water cycle of Stockholm, Sweden.

PubMed

Wahlberg, C; Björlenius, B; Paxéus, N

2011-01-01

Mass flows of 13 pharmaceutical active ingredients (APIS) found in drinking water were studied in the water cycle of Stockholm. Data were collected by analyzing samples of surface water, raw water and drinking water as well as influents, effluents and sludges from waste water treatment plants (WWTPs) in Stockholm area. A mass balance was performed, based on sold amounts of pharmaceuticals and the measured concentrations in water and sludge. The selected APls were all present in WWTP effluents and the removal rates for many of them were poor. Mass balance calculations showed that the three studied WWTPs in Stockholm release considerable amounts of the selected APIs into the Baltic Sea while the portions ending up in WWTP sludge were significantly lower. The levels of APIs found in drinking water are low at present, but may increase in the future unless the releases from WWTPs in the catchment of Lake Mälären are mitigated.

Beginning the 21st century with advanced Automatic Parts Identification (API)

NASA Technical Reports Server (NTRS)

Schramm, Fred; Roxby, Don

1994-01-01

Under the direction of the NASA George C. Marshall Space Flight Center, Huntsville, Alabama, the development and commercialization of an advanced Automated Parts Indentification (API) system is being undertaken by Rockwell International Corporation. The new API system is based on a variable sized, machine-readable, two-dimensioanl matrix symbol that can be applied directly onto most metallic and nonmetallic materials using safe, permanent marking methods. Its checkerboard-like structure is the most space efficient of all symbologies. This high data-density symbology can be applied to products of different material sizes and geometries using application-dependent, computer-driven marking devices. The high fidelity markings produced by these devices can then be captured using a specially designed camera linked to any IBM-compatible computer. Applications of compressed symbology technology will reduce costs and improve quality, productivity, and processes in a wide variety of federal and commercial applications.

The ESGF Software Stack: a Configurable and Extensible Framework for Enabling Access to Geospatial Data

NASA Astrophysics Data System (ADS)

Cinquini, L.; Bell, G. M.; Williams, D.; Harney, J.

2012-12-01

The Earth System Grid Federation (ESGF) is a multi-agency, international collaboration that aims at developing state-of-the-art services for the management and access of Earth system data. ESGF is currently used to serve the totality of the model output used for the forthcoming IPCC 5th assessment report on climate change, as well as supporting observational and reanalysis datasets. Also, it is been adopted by several other projects that focus on global, regional and local climate modeling. The ESGF software stack is composed of several modular applications that cover related but disjoint areas of functionality: data publishing, data search and discovery, data access, user management, security, and federation. Overall, the ESGF infrastructure offers a configurable end-to-end solution to the problem of enabling web-based access to large amounts of geospatial data. This talk will present the architectural and configuration options that are available to a data provider leveraging ESGF to serve their data: which services to expose, how to scale to larger data collections, how to establish access control, how to customize the user interface, and others. Additionally, the framework provides extension points that allow each site to plug in custom functionality such as crawling of specific metadata repositories, exposing domain-specific analysis and visualization services, developing custom access clients that interact with the system APIs. These configuration and extension capabilities are based on simple but effective domain-specific object models, that underpin the software applications: the data model, the security model, and the federation model. The ESGF software stack is developed collaboratively by software engineers at many institutions around the world, and is made freely available to the community under an open source license to promote adoption, reuse, inspection and continuous improvement.

Off-the-shelf mobile handset environments for deploying accelerometer based gait and activity analysis algorithms.

PubMed

Hynes, Martin; Wang, Han; Kilmartin, Liam

2009-01-01

Over the last decade, there has been substantial research interest in the application of accelerometry data for many forms of automated gait and activity analysis algorithms. This paper introduces a summary of new "of-the-shelf" mobile phone handset platforms containing embedded accelerometers which support the development of custom software to implement real time analysis of the accelerometer data. An overview of the main software programming environments which support the development of such software, including Java ME based JSR 256 API, C++ based Motion Sensor API and the Python based "aXYZ" module, is provided. Finally, a sample application is introduced and its performance evaluated in order to illustrate how a standard mobile phone can be used to detect gait activity using such a non-intrusive and easily accepted sensing platform.

Magnetic Material Arrangement In Apis Mellifera Abdomens

DTIC Science & Technology

2002-04-01

UNCLASSIFIED Defense Technical Information Center Compilation Part Notice ADP014406 TITLE: Magnetic Material Arrangement In Apis Mellifera Abdomens...Magnetic Material Arrangement In Apis Mellifera Abdomens Darci M. S. Esquivel, Eliane Wajnberg, Geraldo R. Cernicchiaro, Daniel Acosta-Avalos’ and B.E...transition (52 K- 91 K). Hysteresis curves of Apis mellifera abdomens organized parallel and perpendicular to the applied magnetic field were obtained

Public evaluation of an announcement of public interests communicated by an AIDS patient.

PubMed

Lau, J T; Cheung, C K

1999-01-01

Announcements of public interests (APIs) on television (TV) have been an important means of AIDS prevention. Recently in Hong Kong, the first API on TV which was communicated by a male AIDS patient, named J.J., was displayed on the screen from April to December, 1995. The objective of this study is to examine the effectiveness of this API, as compared with other APIs previously shown in Hong Kong. Collecting data from a random sample of 1,275 residential respondents in Hong Kong through a telephone survey, this study demonstrated that the public gave very favorable evaluation on J.J.'s API, when compared with other APIs. Remarkable impacts of J.J.'s API on the public included increasing concern for AIDS, condom use, and testing blood for HIV infection, and reducing the number of sex partners. The impacts tended to be more salient on male than female viewers. Some of these impacts also appeared to vary by different levels of education and family income.

GIANT API: an application programming interface for functional genomics

PubMed Central

Roberts, Andrew M.; Wong, Aaron K.; Fisk, Ian; Troyanskaya, Olga G.

2016-01-01

GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. PMID:27098035

Can the Air Pollution Index be used to communicate the health risks of air pollution?

PubMed

Li, Li; Lin, Guo-Zhen; Liu, Hua-Zhang; Guo, Yuming; Ou, Chun-Quan; Chen, Ping-Yan

2015-10-01

The validity of using the Air Pollution Index (API) to assess health impacts of air pollution and potential modification by individual characteristics on air pollution effects remain uncertain. We applied distributed lag non-linear models (DLNMs) to assess associations of daily API, specific pollution indices for PM10, SO2, NO2 and the weighted combined API (APIw) with mortality during 2003-2011 in Guangzhou, China. An increase of 10 in API was associated with a 0.88% (95% confidence interval (CI): 0.50, 1.27%) increase of non-accidental mortality at lag 0-2 days. Harvesting effects appeared after 2 days' exposure. The effect estimate of API over lag 0-15 days was statistically significant and similar with those of pollutant-specific indices and APIw. Stronger associations between API and mortality were observed in the elderly, females and residents with low educational attainment. In conclusion, the API can be used to communicate health risks of air pollution. Copyright © 2015 Elsevier Ltd. All rights reserved.

Construct exploit constraint in crash analysis by bypassing canary

NASA Astrophysics Data System (ADS)

Huang, Ning; Huang, Shuguang; Huang, Hui; Chang, Chao

2017-08-01

Selective symbolic execution is a common program testing technology. Developed on the basis of it, some crash analysis systems are often used to test the fragility of the program by constructing exploit constraints, such as CRAX. From the study of crash analysis based on symbolic execution, this paper find that this technology cannot bypass the canary stack protection mechanisms. This paper makes the improvement uses the API hook in Linux. Experimental results show that the use of API hook can effectively solve the problem that crash analysis cannot bypass the canary protection.

Evaluation of API 20E strips for identification of coagulase-negative staphylococci from the urinary tract.

PubMed

Anderson, D Y; Vredeveld, G N; Brake, S R; Buchanan, T F; Lewis, J F

1983-12-01

A previous study indicated that the API 230E system can identify coagulase-negative Staphylococcus species. A study was devised to evaluate the use of the API 20E system for this purpose. Because of the current interest in Staphylococcus saprophyticus the relationship of the API 20E results to novobiocin susceptibility was also examined. One hundred forty-nine isolates of coagulase-negative staphylococci from urine cultures were tested with the API 20E system. The identification of 49 isolates was confirmed by Kloos and Schleifer method. We found that the routine API 20E system did not provide more information than novobiocin susceptibility studies alone, and that there was good but not absolute correlation between novobiocin resistance and identification of S. saprophyticus.

Vocabulary services to support scientific data interoperability

NASA Astrophysics Data System (ADS)

Cox, Simon; Mills, Katie; Tan, Florence

2013-04-01

Shared vocabularies are a core element in interoperable systems. Vocabularies need to be available at run-time, and where the vocabularies are shared by a distributed community this implies the use of web technology to provide vocabulary services. Given the ubiquity of vocabularies or classifiers in systems, vocabulary services are effectively the base of the interoperability stack. In contemporary knowledge organization systems, a vocabulary item is considered a concept, with the "terms" denoting it appearing as labels. The Simple Knowledge Organization System (SKOS) formalizes this as an RDF Schema (RDFS) application, with a bridge to formal logic in Web Ontology Language (OWL). For maximum utility, a vocabulary should be made available through the following interfaces: * the vocabulary as a whole - at an ontology URI corresponding to a vocabulary document * each item in the vocabulary - at the item URI * summaries, subsets, and resources derived by transformation * through the standard RDF web API - i.e. a SPARQL endpoint * through a query form for human users. However, the vocabulary data model may be leveraged directly in a standard vocabulary API that uses the semantics provided by SKOS. SISSvoc3 [1] accomplishes this as a standard set of URI templates for a vocabulary. Any URI comforming to the template selects a vocabulary subset based on the SKOS properties, including labels (skos:prefLabel, skos:altLabel, rdfs:label) and a subset of the semantic relations (skos:broader, skos:narrower, etc). SISSvoc3 thus provides a RESTFul SKOS API to query a vocabulary, but hiding the complexity of SPARQL. It has been implemented using the Linked Data API (LDA) [2], which connects to a SPARQL endpoint. By using LDA, we also get content-negotiation, alternative views, paging, metadata and other functionality provided in a standard way. A number of vocabularies have been formalized in SKOS and deployed by CSIRO, the Australian Bureau of Meteorology (BOM) and their collaborators using SISSvoc3, including: * geologic timescale (multiple versions) * soils classification * definitions from OGC standards * geosciml vocabularies * mining commodities * hyperspectral scalars Several other agencies in Australia have adopted SISSvoc3 for their vocabularies. SISSvoc3 differs from other SKOS-based vocabulary-access APIs such as GEMET [3] and NVS [4] in that (a) the service is decoupled from the content store, (b) the service URI is independent of the content URIs This means that a SISSvoc3 interface can be deployed over any SKOS vocabulary which is available at a SPARQL endpoint. As an example, a SISSvoc3 query and presentation interface has been deployed over the NERC vocabulary service hosted by the BODC, providing a search interface which is not available natively. We use vocabulary services to populate menus in user interfaces, to support data validation, and to configure data conversion routines. Related services built on LDA have also been used as a generic registry interface, and extended for serving gazetteer information. ACKNOWLEDGEMENTS The CSIRO SISSvoc3 implementation is built using the Epimorphics ELDA platform http://code.google.com/p/elda/. We thank Jacqui Githaiga and Terry Rankine for their contributions to SISSvoc design and implementation. REFERENCES 1. SISSvoc3 Specification https://www.seegrid.csiro.au/wiki/Siss/SISSvoc30Specification 2. Linked Data API http://code.google.com/p/linked-data-api/wiki/Specification 3. GEMET https://svn.eionet.europa.eu/projects/Zope/wiki/GEMETWebServiceAPI 4. NVS 2.0 http://vocab.nerc.ac.uk/

Comparing Emerging XML Based Formats from a Multi-discipline Perspective

NASA Astrophysics Data System (ADS)

Sawyer, D. M.; Reich, L. I.; Nikhinson, S.

2002-12-01

This paper analyzes the similarity and differences among several examples of an emerging generation of Scientific Data Formats that are based on XML technologies. Some of the factors evaluated include the goals of these efforts, the data models, and XML technologies used, and the maturity of currently available software. This paper then investigates the practicality of developing a single set of structural data objects and basic scientific concepts, such as units, that could be used across discipline boundaries and extended by disciplines and missions to create Scientific Data Formats for their communities. This analysis is partly based on an effort sponsored by the ESDIS office at GSFC to compare the Earth Science Markup Language (ESML) and the eXtensible Data Format( XDF), two members of this new generation of XML based Data Description Languages that have been developed by NASA funded efforts in recent years. This paper adds FITSML and potentially CDFML to the list of XML based Scientific Data Formats discussed. This paper draws heavily a Formats Evolution Process Committee (http://ssdoo.gsfc.nasa.gov/nost/fep/) draft white paper primarily developed by Lou Reich, Mike Folk and Don Sawyer to assist the Space Science community in understanding Scientific Data Formats. One of primary conclusions of that paper is that a scientific data format object model should be examined along two basic axes. The first is the complexity of the computer/mathematical data types supported and the second is the level of scientific domain specialization incorporated. This paper also discusses several of the issues that affect the decision on whether to implement a discipline or project specific Scientific Data Format as a formal extension of a general purpose Scientific Data Format or to implement the APIs independently.

Use of PCR-restriction fragment length polymorphism analysis for identification of yeast species isolated from bovine intramammary infection.

PubMed

Fadda, M E; Pisano, M B; Scaccabarozzi, L; Mossa, V; Deplano, M; Moroni, P; Liciardi, M; Cosentino, S

2013-01-01

This study reports a rapid PCR-based technique using a one-enzyme RFLP for discrimination of yeasts isolated from bovine clinical and subclinical mastitis milk samples. We analyzed a total of 1,486 milk samples collected over 1 yr in south Sardinia and northern Italy, and 142 yeast strains were preliminarily grouped based on their cultural morphology and physiological characteristics. Assimilation tests were conducted using the identification kit API ID 32C and APILAB Plus software (bioMérieux, Marcy l'Etoile, France). For PCR-RFLP analysis, the 18S-ITS1-5.8S ribosomal(r)DNA region was amplified and then digested with HaeIII, and dendrogram analysis of RFLP fragments was carried out. Furthermore, within each of the groups identified by the API or PCR-RFLP methods, the identification of isolates was confirmed by sequencing of the D1/D2 region using an ABI Prism 310 automatic sequencer (Applied Biosystems, Foster City, CA). The combined phenotypic and molecular approach enabled the identification of 17 yeast species belonging to the genera Candida (47.9%), Cryptococcus (21.1%), Trichosporon (19.7%), Geotrichum (7.1%), and Rhodotorula (4.2%). All Candida species were correctly identified by the API test and their identification confirmed by sequencing. All strains identified with the API system as Geotrichum candidum, Cryptococcus uniguttulatus, and Rhodotorula glutinis also produced characteristic restriction patterns and were confirmed as Galactomyces geotrichum (a teleomorph of G. candidum), Filobasidium uniguttulatum (teleomorph of Crypt. uniguttulatus), and R. glutinis, respectively, by D1/D2 rDNA sequencing. With regard to the genus Trichosporon, preliminary identification by API was problematic, whereas the RFLP technique used in this study gave characteristic restriction profiles for each species. Moreover, sequencing of the D1/D2 region allowed not only successful identification of Trichosporon gracile where API could not, but also correct identification of misidentified isolates. In conclusion, the 18S-ITS1-5.8S region appears to be useful in detecting genetic variability among yeast species, which is valuable for taxonomic purposes and for species identification. We have established an RFLP database for yeast species identified in milk samples using the software GelCompar II and the RFLP database constitutes an initial method for veterinary yeast identification. Copyright © 2013 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Malaria burden and treatment targets in Kachin Special Region II, Myanmar from 2008 to 2016: A retrospective analysis

PubMed Central

Bi, Yaw

2018-01-01

Although drug-based treatment is the primary intervention for malaria control and elimination, optimal use of targeted treatments remains unclear. From 2008 to 2016, three targeted programs on treatment were undertaken in Kachin Special Region II (KR2), Myanmar. Program I (2008–2011) treated all confirmed, clinical and suspected cases; program II (2012–2013) treated confirmed and clinical cases; and program III (2014–2016) targeted confirmed cases only. This study aims to evaluate the impacts of the three programs on malaria burden individually based on the annual parasite incidence (API), slide positivity rate (SPR) and their relative values. The API is calculated from original collected data and the incidence rate ratio (IRR) for each year is calculated by using the first-year API as a reference in each program phase across the KR2. Same method is applied to calculate SPR and risk ratio (RR) at the sentinel hospital too. During program I (2008–2011), malaria burden was reduced by 61% (95%CI: 58%-74%) and the actual API decreased from 9.8 (95%CI: 9.6–10.1) per 100 person-years in 2008 to 3.8 (3.6–4.1) per 100 person-years in 2011. Amid program II (2012–2013), the malaria burden increased by 33% (95%CI: 22%-46%) and the actual API increased from 2.1(95%CI: 2.0–2.3) per 100 person-years in 2012 to 2.8 (95%CI: 2.7–2.9) per 100 person-years in 2013. During program III (2014–2016) the malaria burden increased furtherly by 60% (95%CI: 51% - 69%) and the actual API increased from 3.2(95%CI: 3.0–3.3) per 100 person-years in 2014 to 5.1 (95%CI: 4.9–5.2) per 100 person-years in 2016. Results of the slide positivity of the sentinel hospital also confirm these results. Resurgence of malaria was mainly due to Plasmodium vivax during program II and III. This study indicates that strategy adopted in program I (2008–2011) should be more appropriate for the KR2. Quality-assured treatment of all confirmed, clinical and suspected malaria cases may be helpful for the reduction of malaria burden. PMID:29614088

Efficient Strategies for Active Interface-Level Network Topology Discovery

DTIC Science & Technology

2013-09-01

Network Information Centre API Application Programming Interface APNIC Asia-Pacific Network Information Centre ARIN American Registry for Internet Numbers...very convenient Application Programming Interface ( API ) for easy primitive implementation. Ark’s API facilitates easy development and rapid...prototyping – important attributes as the char- acteristics of our primitives evolve. The API allows a high-level of abstraction, which in turn leads to rapid

Single-step GBLUP using APY inverse for protein yield in US Holstein with a large number of genotyped animals

USDA-ARS?s Scientific Manuscript database

The objective of this study was to provide initial results in an application of single-step genomic BLUP with a genomic relationship matrix (G^-1APY) calculated using the Algorithm of Proven and Young (APY) to 305-day protein yield for US Holsteins. Two G^-1APY were tested; one was from 139,057 geno...

Investigation of the capacity of low glass transition temperature excipients to minimize amorphization of sulfadimidine on comilling.

PubMed

Curtin, Vincent; Amharar, Youness; Hu, Yun; Erxleben, Andrea; McArdle, Patrick; Caron, Vincent; Tajber, Lidia; Corrigan, Owen I; Healy, Anne Marie

2013-01-07

The coprocessing of active pharmaceutical ingredient (API) with an excipient which has a high glass transition temperature (T(g)) is a recognized strategy to stabilize the amorphous form of a drug. This work investigates whether coprocessing a model API, sulfadimidine (SDM) with a series of low T(g) excipients, prevents or reduces amorphization of the crystalline drug. It was hypothesized that these excipients could exert a T(g) lowering effect, resulting in composite T(g) values lower than that of the API alone and promote crystallization of the drug. Milled SDM and comilled SDM with glutaric acid (GA), adipic acid (AA), succinic acid (SA), and malic acid (MA) were characterized with respect to their thermal, X-ray diffraction, spectroscopic, and vapor sorption properties. SDM was predominantly amorphous when milled alone, with an amorphous content of 82%. No amorphous content was detected by dynamic vapor sorption (DVS) on comilling SDM with 50% w/w GA, and amorphous content of the API was reduced by almost 30%, relative to the API milled alone, on comilling with 50% w/w AA. In contrast, amorphization of SDM was promoted on comilling with 50% w/w SA and MA, as indicated by near-infrared (NIR) spectroscopy. Results indicated that the API was completely amorphized in the SDM:MA comilled composite. The saturated solubility of GA and AA in the amorphous API was estimated by thermal methods. It was observed that the T(g) of the comelt quenched composites reached a minimum and leveled out at this solubility concentration. Maximum crystallinity of API on comilling was reached at excipient concentrations comparable to the saturated concentration solubility of excipient in the API. Moreover, the closer the Hildebrand solubility parameter of the excipient to the API, the greater the inhibition of API amorphization on comilling. The results reported here indicate that an excipient with a low T(g) coupled with high solubility in the API can prevent or reduce the generation of an amorphous phase on comilling.

Ethanol-Induced Effects on Sting Extension Response and Punishment Learning in the Western Honey Bee (Apis mellifera)

PubMed Central

Giannoni-Guzmán, Manuel A.; Giray, Tugrul; Agosto-Rivera, Jose Luis; Stevison, Blake K.; Freeman, Brett; Ricci, Paige; Brown, Erika A.; Abramson, Charles I.

2014-01-01

Acute ethanol administration is associated with sedation and analgesia as well as behavioral disinhibition and memory loss but the mechanisms underlying these effects remain to be elucidated. During the past decade, insects have emerged as important model systems to understand the neural and genetic bases of alcohol effects. However, novel assays to assess ethanol's effects on complex behaviors in social or isolated contexts are necessary. Here we used the honey bee as an especially relevant model system since bees are typically exposed to ethanol in nature when collecting standing nectar crop of flowers, and there is recent evidence for independent biological significance of this exposure for social behavior. Bee's inhibitory control of the sting extension response (SER) and a conditioned-place aversion assay were used to study ethanol effects on analgesia, behavioral disinhibition, and associative learning. Our findings indicate that although ethanol, in a dose-dependent manner, increases SER thresholds (analgesic effects), it disrupts the ability of honey bees to inhibit SER and to associate aversive stimuli with their environment. These results suggest that ethanol's effects on analgesia, behavioral disinhibition and associative learning are common across vertebrates and invertebrates. These results add to the use of honey bees as an ethanol model to understand ethanol's effects on complex, socially relevant behaviors. PMID:24988309

Comparative virulence and competition between Nosema apis and Nosema ceranae in honey bees (Apis mellifera).

PubMed

Milbrath, Meghan O; van Tran, Toan; Huang, Wei-Fong; Solter, Leellen F; Tarpy, David R; Lawrence, Frank; Huang, Zachary Y

2015-02-01

Honey bees (Apis mellifera) are infected by two species of microsporidia: Nosema apis and Nosemaceranae. Epidemiological evidence indicates that N. ceranae may be replacing N. apis globally in A. mellifera populations, suggesting a potential competitive advantage of N. ceranae. Mixed infections of the two species occur, and little is known about the interactions among the host and the two pathogens that have allowed N. ceranae to become dominant in most geographical areas. We demonstrated that mixed Nosema species infections negatively affected honey bee survival (median survival=15-17days) more than single species infections (median survival=21days and 20days for N. apis and N. ceranae, respectively), with median survival of control bees of 27days. We found similar rates of infection (percentage of bees with active infections after inoculation) for both species in mixed infections, with N. apis having a slightly higher rate (91% compared to 86% for N. ceranae). We observed slightly higher spore counts in bees infected with N. ceranae than in bees infected with N. apis in single microsporidia infections, especially at the midpoint of infection (day 10). Bees with mixed infections of both species had higher spore counts than bees with single infections, but spore counts in mixed infections were highly variable. We did not see a competitive advantage for N. ceranae in mixed infections; N. apis spore counts were either higher or counts were similar for both species and more N. apis spores were produced in 62% of bees inoculated with equal dosages of the two microsporidian species. N. ceranae does not, therefore, appear to have a strong within-host advantage for either infectivity or spore growth, suggesting that direct competition in these worker bee mid-guts is not responsible for its apparent replacement of N. apis. Copyright © 2014 Elsevier Inc. All rights reserved.

An example of how to handle amorphous fractions in API during early pharmaceutical development: SAR114137--a successful approach.

PubMed

Petzoldt, Christine; Bley, Oliver; Byard, Stephen J; Andert, Doris; Baumgartner, Bruno; Nagel, Norbert; Tappertzhofen, Christoph; Feth, Martin Philipp

2014-04-01

The so-called pharmaceutical solid chain, which encompasses drug substance micronisation to the final tablet production, at pilot plant scale is presented as a case study for a novel, highly potent, pharmaceutical compound: SAR114137. Various solid-state analytical methods, such as solid-state Nuclear Magnetic Resonance (ssNMR), Differential Scanning Calorimetry (DSC), Dynamic Water Vapour Sorption Gravimetry (DWVSG), hot-stage Raman spectroscopy and X-ray Powder Diffraction (XRPD) were applied and evaluated to characterise and quantify amorphous content during the course of the physical treatment of crystalline active pharmaceutical ingredient (API). DSC was successfully used to monitor the changes in amorphous content during micronisation of the API, as well as during stability studies. (19)F solid-state NMR was found to be the method of choice for the detection and quantification of low levels of amorphous API, even in the final drug product (DP), since compaction during tablet manufacture was identified as a further source for the formation of amorphous API. The application of different jet milling techniques was a critical factor with respect to amorphous content formation. In the present case, the change from spiral jet milling to loop jet milling led to a decrease in amorphous API content from 20-30 w/w% to nearly 0 w/w% respectively. The use of loop jet milling also improved the processability of the API. Stability investigations on both the milled API and the DP showed a marked tendency for recrystallisation of the amorphous API content on exposure to elevated levels of relative humidity. No significant impact of amorphous API on either the chemical stability or the dissolution rate of the API in drug formulation was observed. Therefore, the presence of amorphous content in the oral formulation was of no consequence for the clinical trial phases I and II. Copyright © 2013 Elsevier B.V. All rights reserved.

Systematic CRISPR-Cas9-Mediated Modifications of Plasmodium yoelii ApiAP2 Genes Reveal Functional Insights into Parasite Development

PubMed Central

Zhang, Cui; Li, Zhenkui; Cui, Huiting; Jiang, Yuanyuan; Yang, Zhenke; Wang, Xu; Gao, Han; Liu, Cong; Zhang, Shujia

2017-01-01

ABSTRACT Malaria parasites have a complex life cycle with multiple developmental stages in mosquito and vertebrate hosts, and different developmental stages express unique sets of genes. Unexpectedly, many transcription factors (TFs) commonly found in eukaryotic organisms are absent in malaria parasites; instead, a family of genes encoding proteins similar to the plant Apetala2 (ApiAP2) transcription factors is expanded in the parasites. Several malaria ApiAP2 genes have been shown to play a critical role in parasite development; however, the functions of the majority of the ApiAP2 genes remain to be elucidated. In particular, no study on the Plasmodium yoelii ApiAP2 (PyApiAP2) gene family has been reported so far. This study systematically investigated the functional roles of PyApiAP2 genes in parasite development. Twenty-four of the 26 PyApiAP2 genes were selected for disruption, and 12 were successfully knocked out using the clustered regularly interspaced short palindromic repeat–CRISPR-associated protein 9 (CRISPR-Cas9) method. The effects of gene knockout (KO) on parasite development in mouse and mosquito stages were evaluated. Ten of 12 successfully disrupted genes, including two genes that have not been functionally characterized in any Plasmodium species previously, were shown to be critical for P. yoelii development of sexual and mosquito stages. Additionally, seven of the genes were labeled for protein expression analysis, revealing important information supporting their functions. This study represents the first systematic functional characterization of the P. yoelii ApiAP2 gene family and discovers important insights on the roles of the ApiAP2 genes in parasite development. PMID:29233900

Pharmacokinetics and Abuse Potential of Benzhydrocodone, a Novel Prodrug of Hydrocodone, After Intranasal Administration in Recreational Drug Users.

PubMed

Mickle, Travis C; Guenther, Sven M; Barrett, Andrew C; Roupe, Kathryn Ann; Zhou, Jing; Dickerson, Daniel; Webster, Lynn R

2017-10-28

Developing an acetaminophen-free, immediate-release hydrocodone product remains an unmet medical need; however, new opioid analgesics should not introduce new abuse risks. Benzhydrocodone is a prodrug of hydrocodone that must be metabolized into hydrocodone by enzymes in the intestinal tract to optimally deliver its pharmacologic effects. This study evaluated the intranasal pharmacokinetics and abuse potential of benzhydrocodone active pharmaceutical ingredient (API) compared with hydrocodone bitartrate (HB) API. Single-center, randomized, double-blind, crossover study. Clinical research site. Healthy adult, nondependent, recreational opioid users. Subjects (N = 51 Completers) were randomized to receive 13.34 mg of intranasal benzhydrocodone API and 15.0 mg of intranasal HB API (molar-equivalent doses of hydrocodone). Blood samples were taken, and Drug Liking scores (assessed on a bipolar visual analog scale) were obtained throughout each dosing interval. Nasal irritation and safety were assessed. Peak hydrocodone plasma concentration (Cmax) was 36.0% lower, and total hydrocodone exposures (AUClast and AUCinf) were 20.3% and 19.5% lower, respectively, for benzhydrocodone API compared with HB API (P < 0.0001). All partial AUC values were lower for benzhydrocodone API, with a ≥ 75% reduction in hydrocodone exposure at all time intervals up to one hour postdose (P < 0.0001). Median Tmax of hydrocodone following benzhydrocodone API was delayed by more than one hour compared with HB. Drug Liking score, as assessed by maximal liking (Emax), was significantly lower for benzhydrocodone API vs HB API (P = 0.004), with 45% of subjects showing a ≥ 30% reduction in Drug Liking Emax. Reductions in hydrocodone exposure and associated decreases in Drug Liking relative to HB suggest that the prodrug benzhydrocodone may deter intranasal abuse. © 2017 American Academy of Pain Medicine.

A family of silver(I) complexes built with 2-sulfoterephthalic acid monosodium salt and different aminopyridine ligands: Syntheses, structures and properties

NASA Astrophysics Data System (ADS)

Zhang, Jie; Tan, Gai-Xiu; Liu, Bao-Lin; Dai, Yu-Bei; Xu, Na; Wen, Wei-Fen; Cao, Chong; Xiao, Hong-Ping

2017-05-01

Five Ag(I) coordination complexes, namely, [Ag6(2-stp)2(3-methyl-2-apy)3·H2O]n (1), [Ag3(2-stp)(4-methyl-2-apy)3]n (2), [Na2Ag18(2-stp)4(2-Hstp)4(5-methyl-2-apy)16 (H2O)4·11H2O]n (3), Ag3(2-stp)(6-methy-2-apy)4·H2O (4), and [Ag6(2-stp)2(6-methyl-2-apy)8(H2O)2·H2O]n (5) (2-NaH2stp = 2-sulfoterephthalic acid monosodium salt, 3-methyl-2-apy = 3-methyl-2-aminopyridine, 4-methyl-2-apy = 4-methyl-2-aminopyridine, 5-methyl-2-apy = 5-methyl-2-aminopyridine, 6-methyl-2-apy = 6-methyl-2-aminopyridine), have been synthesized and structurally characterized. Complexes 1 and 2 show two-dimensional network. In complex 3, the adjacent Ag10 units are bridged by 5-methyl-2-apy ligands to form a 2D infinite undulated sheet. Adjacent 2D sheets are linked by coordinative bonds between carboxylic oxygen atoms and Na(I) ions to form a 3D coordination polymer. Complex 4 is a 0-D discrete trinuclear molecule, and the self-complementary the Osbnd H⋯O and Nsbnd H⋯O hydrogen bonds incorporating hydrogen bond motifs extend these molecules into a 2D supramolecular framework. Compound 5 exhibits 1D-chain structure. However, complex 5 shows 3D supramolecular structure results from the linkage of neighboring layers through a rich hydrogen-bonding between uncoordinated sulfonates, amino groups and coordinated carboxylates. The thermogravimetric analyses and photoluminescence of the complexes were also investigated.

Artificial periodic irregularities in the high-latitude ionosphere excited by the HAARP facility

NASA Astrophysics Data System (ADS)

Bakhmetieva, N. V.; Grach, S. M.; Sergeev, E. N.; Shindin, A. V.; Milikh, G. M.; Siefring, C. L.; Bernhardt, P. A.; McCarrick, M.

2016-07-01

We present results of the new observations of artificial periodic irregularities (APIs) in the ionosphere using the High Frequency Active Auroral Research Program (HAARP) heating facility carried out in late May and early June 2014.The objective of this work is to detect API using high-latitude facility and analyze possible differences of the temporal and spatial variations of the API echoes in the high (HAARP) and middle (Sura) latitudes. Irregularities were created by the powerful wave of X mode and were sounded using the short probing pulses signals of X mode. API echoes were observed in the D, E, and F regions of the ionosphere. Amplitudes and characteristic times of the API echoes were measured. The API growth and decay times at HAARP (high latitudes) observed were similar to those at the Sura heating facility (midlatitudes).

The geospatial data quality REST API for primary biodiversity data

PubMed Central

Otegui, Javier; Guralnick, Robert P.

2016-01-01

Summary: We present a REST web service to assess the geospatial quality of primary biodiversity data. It enables access to basic and advanced functions to detect completeness and consistency issues as well as general errors in the provided record or set of records. The API uses JSON for data interchange and efficient parallelization techniques for fast assessments of large datasets. Availability and implementation: The Geospatial Data Quality API is part of the VertNet set of APIs. It can be accessed at http://api-geospatial.vertnet-portal.appspot.com/geospatial and is already implemented in the VertNet data portal for quality reporting. Source code is freely available under GPL license from http://www.github.com/vertnet/api-geospatial. Contact: javier.otegui@gmail.com or rguralnick@flmnh.ufl.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26833340

The geospatial data quality REST API for primary biodiversity data.

PubMed

Otegui, Javier; Guralnick, Robert P

2016-06-01

We present a REST web service to assess the geospatial quality of primary biodiversity data. It enables access to basic and advanced functions to detect completeness and consistency issues as well as general errors in the provided record or set of records. The API uses JSON for data interchange and efficient parallelization techniques for fast assessments of large datasets. The Geospatial Data Quality API is part of the VertNet set of APIs. It can be accessed at http://api-geospatial.vertnet-portal.appspot.com/geospatial and is already implemented in the VertNet data portal for quality reporting. Source code is freely available under GPL license from http://www.github.com/vertnet/api-geospatial javier.otegui@gmail.com or rguralnick@flmnh.ufl.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

HIV testing among sexually experienced Asian and Pacific Islander young women association with routine gynecologic care.

PubMed

Hahm, Hyeouk Chris; Song, In Han; Ozonoff, Al; Sassani, Jessica C

2009-01-01

To describe the proportion of HIV testing in the past 12 months among sexually experienced Asian and Pacific Islander (API) women and to investigate to what extent routine gynecologic care (RGC) increases HIV testing among API women. Data were derived from Wave III of the National Longitudinal Study of Adolescent Health (Add Health). Analyses were limited to 7,576 sexually experienced women (White, n = 4,482 [68.5%]; Black, n = 1,693 [25.6%]; Hispanic, n = 923 [13.9%]; API, n = 478 [7.2%]) aged 18-27 years. Multiple logistic regression analyses were used to estimate the association between RGC and HIV testing after controlling for predisposing, need, and enabling factors. On average, 22.8% (n = 1,504) of sexually experienced women reported HIV testing in the past year. API women had the lowest proportion of testing (17.2%), and Black women had the highest (26.2%). Overall, 60.2% of API women reported receiving RGC; however, only 15.5% of API who received RGC reported HIV testing. After controlling for covariates, significantly positive associations were found for White, Black, and Hispanic women between RGC and HIV testing; however, there was no evidence that RGC was associated with HIV testing among API women. Our data suggest that RGC does not [corrected] increase HIV testing among API women. To eliminate disparities in HIV testing service utilization among API women, appropriate efforts should be directed to better understand the barriers and facilitators of HIV testing among this population.

Determination of sorption of seventy-five pharmaceuticals in sewage sludge.

PubMed

Hörsing, Maritha; Ledin, Anna; Grabic, Roman; Fick, Jerker; Tysklind, Mats; la Cour Jansen, Jes; Andersen, Henrik R

2011-10-01

Sorption of 75 active pharmaceutical ingredients (APIs) to three different types of sludge (primary sludge, secondary sludge with short and long sludge age respectively) were investigated. To obtain the sorption isotherms batch studies with the APIs mixture were performed in four nominal concentrations to water containing 1 g of sludge. The range of APIs concentrations was between ng L(-1) to μg L(-1) which are found in the wastewater effluents. Isotherms were obtained for approximately 45 of the APIs, providing distribution coefficients for linear (Kd), Freundlich (Kf) and Langmuir (KL) isotherms. Kd, Kf and KL ranging between 7.1×10(4) and 3.8×10(7), 1.1×10(-2) and 6.1×10(4) and 9.2×10(-3) and 1.1 L kg(-1), respectively. The obtained coefficients were applied to estimate the fraction of APIs in the water phase (see Abstract Graphic). For 37 of the 75 APIs, the predicted presence in the liquid phase was estimated to >80%. 24 APIs were estimated to be present in the liquid phase between 20 and 80%, and 14 APIs were found to have <20% presence in the liquid phase, i.e. high affinity towards sludge. Furthermore, the effect of pH at values 6, 7 and 8 was evaluated using one way ANOVA-test. A significant difference in Kds due to pH changes were found for 6 of the APIs (variation 10-20%). Copyright © 2011 Elsevier Ltd. All rights reserved.

Sorption of active pharmaceutical ingredients in untreated wastewater effluent and effect of dilution in freshwater: Implications for an "impact zone" environmental risk assessment approach.

PubMed

Bagnis, Simone; Fitzsimons, Mark; Snape, Jason; Tappin, Alan; Comber, Sean

2018-05-15

Evidence of ecotoxicological effects of active pharmaceuticals ingredients (APIs) has increased research into their environmental fate. In low and low-middle income countries (LLMICs) the main source of APIs to surface waters is from discharge of untreated wastewater. Consequently, concentrations of APIs can be relatively high in the "impact zone" downstream of a discharge point. Little is known about the fate of APIs in these impact zones. In this laboratory scale investigation, the effect of successive dilution of synthetic untreated wastewater (dilution factor 1 to 10) on the distribution of APIs was studied. The sorption was consistent with the chemical properties of each compound: charge, lipophilicity, and structure. Dilution increased desorption of the basic and neutral APIs (up to 27.7%) and correlated with their lipophilicity (R 2 >0.980); the positive charge was of secondary importance. Anions did not significantly desorb (<10% loss). Increased concentrations of dissolved organic matter at dilutions of 8 and 10 times that of untreated wastewater coincided with lower dissolved API concentrations. The data showed a clear trend in the desorption process of APIs that may lead to higher exposure risk than anticipated. Therefore, it is suggested that these aspects should be accounted for in the development of dedicated environmental risk assessment approach for APIs in riverine impact zones of LLMICs countries. Copyright © 2017 Elsevier B.V. All rights reserved.

Preclinical Bioavailability Strategy for Decisions on Clinical Drug Formulation Development: An In Depth Analysis.

PubMed

Van den Bergh, An; Van Hemelryck, Sandy; Bevernage, Jan; Van Peer, Achiel; Brewster, Marcus; Mackie, Claire; Mannaert, Erik

2018-06-11

The aim of the presented retrospective analysis was to verify whether a previously proposed Janssen Biopharmaceutical Classification System (BCS)-like decision tree, based on preclinical bioavailability data of a solution and suspension formulation, would facilitate informed decision making on the clinical formulation development strategy. In addition, the predictive value of (in vitro) selection criteria, such as solubility, human permeability, and/or a clinical dose number (Do), were evaluated, potentially reducing additional supporting formulation bioavailability studies in animals. The absolute ( F abs,sol ) and relative ( F rel, susp/sol ) bioavailability of an oral solution and suspension, respectively, in rat or dog and the anticipated BCS classification were analyzed for 89 Janssen compounds with 28 of these having F rel,susp/sol and F abs,sol in both rat and dog at doses around 10 and 5 mg/kg, respectively. The bioavailability outcomes in the dog aligned well with a BCS-like classification based upon the solubility of the active pharmaceutical ingredient (API) in biorelevant media, while the alignment was less clear for the bioavailability data in the rat. A retrospective analysis on the clinically tested formulations for a set of 12 Janssen compounds confirmed that the previously proposed animal bioavailability-based decision tree facilitated decisions on the oral formulation type, with the dog as the most discriminative species. Furthermore, the analysis showed that based on a Do for a standard human dose of 100 mg in aqueous and/or biorelevant media, a similar formulation type would have been selected compared to the one suggested by the animal data. However, the concept of a Do did not distinguish between solubility enhancing or enabling formulations and does not consider the API permeability, and hence, it produces the risk of slow and potentially incomplete oral absorption of an API with poor intestinal permeability. In cases where clinical dose estimations are available early in development, the preclinical bioavailability studies and dose number calculations, used to guide formulation selection, may be performed at more relevant doses instead of the proposed standard human dose. It should be noted, however, that unlike in late development, there is uncertainty on the clinical dose estimated in the early clinical phases because that dose is usually only based on in vitro and/or in vivo animal pharmacology models, or early clinical biomarker information. Therefore, formulation strategies may be adjusted based on emerging data supporting clinical doses. In summary, combined early information on in vitro-assessed API solubility and permeability, preclinical suspension/solution bioavailability data in relation to the intravenous clearance, and metabolic pathways of the API can strengthen formulation decisions. However, these data may not always fully distinguish between conventional (e.g., to be taken with food), enhancing, and enabling formulations. Therefore, to avoid overinvestment in complex and expensive enabling technologies, it is useful to evaluate a conventional and solubility (and/or permeability) enhancing formulation under fasted and fed conditions, as part of a first-in-human study or in a subsequent early human bioavailability study, for compounds with high Do, a low animal F rel,susp/sol , or low F abs,sol caused by precipitation of the solubilized API.

Identification of Complete Repertoire of Apis florea Odorant Receptors Reveals Complex Orthologous Relationships with Apis mellifera

PubMed Central

Karpe, Snehal D.; Jain, Rikesh; Brockmann, Axel; Sowdhamini, Ramanathan

2016-01-01

Abstract We developed a computational pipeline for homology based identification of the complete repertoire of olfactory receptor (OR) genes in the Asian honey bee species, Apis florea. Apis florea is phylogenetically the most basal honey bee species and also the most distant sister species to the Western honey bee Apis mellifera, for which all OR genes had been identified before. Using our pipeline, we identified 180 OR genes in A. florea, which is very similar to the number of ORs identified in A. mellifera (177 ORs). Many characteristics of the ORs including gene structure, synteny of tandemly repeated ORs and basic phylogenetic clustering are highly conserved. The composite phylogenetic tree of A. florea and A. mellifera ORs could be divided into 21 clades which are in harmony with the existing Hymenopteran tree. However, we found a few nonorthologous OR relationships between both species as well as independent pseudogenization of ORs suggesting separate evolutionary changes. Particularly, a subgroup of the OR gene clade XI, which had been hypothesized to code cuticular hydrocarbon receptors showed a high number of species-specific ORs. RNAseq analysis detected a total number of 145 OR transcripts in male and 162 in female antennae. Most of the OR genes were highly expressed on the female antennae. However, we detected five distinct male-biased OR genes, out of which three genes (AfOr11, AfOr18, AfOr170P) were shown to be male-biased in A. mellifera, too, thus corroborating a behavioral function in sex-pheromone communication. PMID:27540087

Twitter data analysis: temporal and term frequency analysis with real-time event

NASA Astrophysics Data System (ADS)

Yadav, Garima; Joshi, Mansi; Sasikala, R.

2017-11-01

From the past few years, World Wide Web (www) has become a prominent and huge source for user generated content and opinionative data. Among various social media, Twitter gained popularity as it offers a fast and effective way of sharing users’ perspective towards various critical and other issues in different domain. As the data is hugely generated on cloud, it has opened doors for the researchers in the field of data science and analysis. There are various domains such as ‘Political’ domain, ‘Entertainment’ domain and ‘Business’ domain. Also there are various APIs that Twitter provides for developers 1) Search API, focus on the old tweets 2) Rest API, focuses on user details and allow to collect the user profile, friends and followers 3) Streaming API, which collects details like tweets, hashtags, geo locations. In our work we are accessing Streaming API in order to fetch real-time tweets for the dynamic happening event. For this we are focusing on ‘Entertainment’ domain especially ‘Sports’ as IPL-T20 is currently the trending on-going event. We are collecting these numerous amounts of tweets and storing them in MongoDB database where the tweets are stored in JSON document format. On this document we are performing time-series analysis and term frequency analysis using different techniques such as filtering, information extraction for text-mining that fulfils our objective of finding interesting moments for temporal data in the event and finding the ranking among the players or the teams based on popularity which helps people in understanding key influencers on the social media platform.

Functional characterization of naturally occurring melittin peptide isoforms in two honey bee species, Apis mellifera and Apis cerana.

PubMed

Park, Doori; Jung, Je Won; Lee, Mi Ok; Lee, Si Young; Kim, Boyun; Jin, Hye Jun; Kim, Jiyoung; Ahn, Young-Joon; Lee, Ki Won; Song, Yong Sang; Hong, Seunghun; Womack, James E; Kwon, Hyung Wook

2014-03-01

Insect-derived antimicrobial peptides (AMPs) have diverse effects on antimicrobial properties and pharmacological activities such as anti-inflammation and anticancer properties. Naturally occurring genetic polymorphism have a direct and/or indirect influence on pharmacological effect of AMPs, therefore information on single nucleotide polymorphism (SNP) occurring in natural AMPs provides an important clue to therapeutic applications. Here we identified nucleotide polymorphisms in melittin gene of honey bee populations, which is one of the potent AMP in bee venoms. We found that the novel SNP of melittin gene exists in these two honey bee species, Apis mellifera and Apis cerana. Nine polymorphisms were identified within the coding region of the melittin gene, of which one polymorphism that resulted in serine (Ser) to asparagine (Asp) substitution that can potentially effect on biological activities of melittin peptide. Serine-substituted melittin (Mel-S) showed more cytotoxic effect than asparagine-substituted melittin (Mel-N) against E. coli. Also, Mel-N and Mel-S had different inhibitory effects on the production of inflammatory factors such as IL-6 and TNF-α in BV-2 cells. Moreover, Mel-S showed stronger cytotoxic activities than Mel-N peptide against two human ovarian cancer cell lines. Using carbon nanotube-based transistor, we here characterized that Mel-S interacted with small unilamellar liposomes more strongly than Mel-N. Taken together, our present study demonstrates that there exist different characteristics of the gene frequency and the biological activities of the melittin peptide in two honey bee species, Apis mellifera and A. cerana. Copyright © 2014 Elsevier Inc. All rights reserved.

The RNASeq-er API-a gateway to systematically updated analysis of public RNA-seq data.

PubMed

Petryszak, Robert; Fonseca, Nuno A; Füllgrabe, Anja; Huerta, Laura; Keays, Maria; Tang, Y Amy; Brazma, Alvis

2017-07-15

The exponential growth of publicly available RNA-sequencing (RNA-Seq) data poses an increasing challenge to researchers wishing to discover, analyse and store such data, particularly those based in institutions with limited computational resources. EMBL-EBI is in an ideal position to address these challenges and to allow the scientific community easy access to not just raw, but also processed RNA-Seq data. We present a Web service to access the results of a systematically and continually updated standardized alignment as well as gene and exon expression quantification of all public bulk (and in the near future also single-cell) RNA-Seq runs in 264 species in European Nucleotide Archive, using Representational State Transfer. The RNASeq-er API (Application Programming Interface) enables ontology-powered search for and retrieval of CRAM, bigwig and bedGraph files, gene and exon expression quantification matrices (Fragments Per Kilobase Of Exon Per Million Fragments Mapped, Transcripts Per Million, raw counts) as well as sample attributes annotated with ontology terms. To date over 270 00 RNA-Seq runs in nearly 10 000 studies (1PB of raw FASTQ data) in 264 species in ENA have been processed and made available via the API. The RNASeq-er API can be accessed at http://www.ebi.ac.uk/fg/rnaseq/api . The commands used to analyse the data are available in supplementary materials and at https://github.com/nunofonseca/irap/wiki/iRAP-single-library . rnaseq@ebi.ac.uk ; rpetry@ebi.ac.uk. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Multicomponent Pharmaceutical Cocrystals: A Novel Approach for Combination Therapy.

PubMed

Fatima, Zeeshan; Srivastava, Dipti; Kaur, Chanchal Deep

2018-03-05

Cocrystallization is a technique for modifying the physicochemical and pharmacokinetic properties of an active pharmaceutical ingredient (API) embodying the concept of supramolecular synthon. Most of the examples cited in the literature are of cocrystals formed between an API and a coformer chosen from the generally recognized as safe (GRAS) substance list, however, few examples exist where a cocrystal consists of two or more APIs. These cocrystals are commonly known as multi API, multi drug or drug- drug cocrystals. The formation of such cocrystals is feasible by virtue of non covalent interactions between the APIs, which help them in retaining their biologic activity. In addition, drug- drug cocrystals also offer the potential solution to the limitations such as solubility, stability differences and chemical interaction between the APIs which is often faced during the traditional combination therapy. Cocrystallization of two or more APIs can be employed for delivery of combination drugs for the better and efficacious management of many complex disorders where existing monotherapies do not furnish the desired therapeutic effect. This review on the existing drug-drug cocrystals is to gain insight for better designing of multi API cocrystals with improved physicochemical and pharmacokinetic profile and its application in multiple target therapy. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Accessing the SEED genome databases via Web services API: tools for programmers.

PubMed

Disz, Terry; Akhter, Sajia; Cuevas, Daniel; Olson, Robert; Overbeek, Ross; Vonstein, Veronika; Stevens, Rick; Edwards, Robert A

2010-06-14

The SEED integrates many publicly available genome sequences into a single resource. The database contains accurate and up-to-date annotations based on the subsystems concept that leverages clustering between genomes and other clues to accurately and efficiently annotate microbial genomes. The backend is used as the foundation for many genome annotation tools, such as the Rapid Annotation using Subsystems Technology (RAST) server for whole genome annotation, the metagenomics RAST server for random community genome annotations, and the annotation clearinghouse for exchanging annotations from different resources. In addition to a web user interface, the SEED also provides Web services based API for programmatic access to the data in the SEED, allowing the development of third-party tools and mash-ups. The currently exposed Web services encompass over forty different methods for accessing data related to microbial genome annotations. The Web services provide comprehensive access to the database back end, allowing any programmer access to the most consistent and accurate genome annotations available. The Web services are deployed using a platform independent service-oriented approach that allows the user to choose the most suitable programming platform for their application. Example code demonstrate that Web services can be used to access the SEED using common bioinformatics programming languages such as Perl, Python, and Java. We present a novel approach to access the SEED database. Using Web services, a robust API for access to genomics data is provided, without requiring large volume downloads all at once. The API ensures timely access to the most current datasets available, including the new genomes as soon as they come online.

Drug Solubility in Fatty Acids as a Formulation Design Approach for Lipid-Based Formulations: A Technical Note.

PubMed

Lee, Yung-Chi; Dalton, Chad; Regler, Brian; Harris, David

2018-06-06

Lipid-based drug delivery systems have been intensively investigated as a means of delivering poorly water-soluble drugs. Upon ingestion, the lipases in the gastrointestinal tract digest lipid ingredients, mainly triglycerides, within the formulation into monoglycerides and fatty acids. While numerous studies have addressed the solubility of drugs in triglycerides, comparatively few publications have addressed the solubility of drugs in fatty acids, which are the end product of digestion and responsible for the solubility of drug within mixed micelles. The objective of this investigation was to explore the solubility of a poorly water-soluble drug in fatty acids and raise the awareness of the importance of drug solubility in fatty acids. The model API (active pharmaceutical ingredient), a weak acid, is considered a BCS II compound with an aqueous solubility of 0.02 μg/mL and predicted partition coefficient >7. The solubility of API ranged from 120 mg/mL to over 1 g/mL in fatty acids with chain lengths across the range C18 to C6. Hydrogen bonding was found to be the main driver of the solubilization of API in fatty acids. The solubility of API was significantly reduced by water uptake in caprylic acid but not in oleic acid. This report demonstrates that solubility data generated in fatty acids can provide an indication of the solubility of the drug after lipid digestion. This report also highlights the importance of measuring the solubility of drugs in fatty acids in the course of lipid formulation development.

Predicting concentrations of trace organic compounds in municipal wastewater treatment plant sludge and biosolids using the PhATE™ model.

PubMed

Cunningham, Virginia L; D'Aco, Vincent J; Pfeiffer, Danielle; Anderson, Paul D; Buzby, Mary E; Hannah, Robert E; Jahnke, James; Parke, Neil J

2012-07-01

This article presents the capability expansion of the PhATE™ (pharmaceutical assessment and transport evaluation) model to predict concentrations of trace organics in sludges and biosolids from municipal wastewater treatment plants (WWTPs). PhATE was originally developed as an empirical model to estimate potential concentrations of active pharmaceutical ingredients (APIs) in US surface and drinking waters that could result from patient use of medicines. However, many compounds, including pharmaceuticals, are not completely transformed in WWTPs and remain in biosolids that may be applied to land as a soil amendment. This practice leads to concerns about potential exposures of people who may come into contact with amended soils and also about potential effects to plants and animals living in or contacting such soils. The model estimates the mass of API in WWTP influent based on the population served, the API per capita use, and the potential loss of the compound associated with human use (e.g., metabolism). The mass of API on the treated biosolids is then estimated based on partitioning to primary and secondary solids, potential loss due to biodegradation in secondary treatment (e.g., activated sludge), and potential loss during sludge treatment (e.g., aerobic digestion, anaerobic digestion, composting). Simulations using 2 surrogate compounds show that predicted environmental concentrations (PECs) generated by PhATE are in very good agreement with measured concentrations, i.e., well within 1 order of magnitude. Model simulations were then carried out for 18 APIs representing a broad range of chemical and use characteristics. These simulations yielded 4 categories of results: 1) PECs are in good agreement with measured data for 9 compounds with high analytical detection frequencies, 2) PECs are greater than measured data for 3 compounds with high analytical detection frequencies, possibly as a result of as yet unidentified depletion mechanisms, 3) PECs are less than analytical reporting limits for 5 compounds with low analytical detection frequencies, and 4) the PEC is greater than the analytical method reporting limit for 1 compound with a low analytical detection frequency, possibly again as a result of insufficient depletion data. Overall, these results demonstrate that PhATE has the potential to be a very useful tool in the evaluation of APIs in biosolids. Possible applications include: prioritizing APIs for assessment even in the absence of analytical methods; evaluating sludge processing scenarios to explore potential mitigation approaches; using in risk assessments; and developing realistic nationwide concentrations, because PECs can be represented as a cumulative probability distribution. Finally, comparison of PECs to measured concentrations can also be used to identify the need for fate studies of compounds of interest in biosolids. Copyright © 2011 SETAC.

Pipe Storage and Movement Study

DTIC Science & Technology

1986-02-01

API 5L Points Higher Price Than API 5L Grades A or B Wall Range—X Grades X42 * X46* X52 * X60 X65 X70* * All Walls...thereof may be used at Mill Option for API 5L Grades X42, X46 and X52 unless specifically prohibited. * * DSAW only. NOTES: For Intermediate Grodes, apply...A53, BW, S 80, GALV 1-1/4", STL, A53, BW, S 80, GALV 2", STL, A53, BW, S 80, GALV 8", STL, API - 5L GR X-42, ERW, STD 3-1/2"OD, STL, API - 5L GR

Tactile learning and the individual evaluation of the reward in honey bees (Apis mellifera L.).

PubMed

Scheiner, R; Erber, J; Page, R E

1999-07-01

Using the proboscis extension response we conditioned pollen and nectar foragers of the honey bee (Apis mellifera L.) to tactile patterns under laboratory conditions. Pollen foragers demonstrated better acquisition, extinction, and reversal learning than nectar foragers. We tested whether the known differences in response thresholds to sucrose between pollen and nectar foragers could explain the observed differences in learning and found that nectar foragers with low response thresholds performed better during acquisition and extinction than ones with higher thresholds. Conditioning pollen and nectar foragers with similar response thresholds did not yield differences in their learning performance. These results suggest that differences in the learning performance of pollen and nectar foragers are a consequence of differences in their perception of sucrose. Furthermore, we analysed the effect which the perception of sucrose reward has on associative learning. Nectar foragers with uniform low response thresholds were conditioned using varying concentrations of sucrose. We found significant positive correlations between the concentrations of the sucrose rewards and the performance during acquisition and extinction. The results are summarised in a model which describes the relationships between learning performance, response threshold to sucrose, concentration of sucrose and the number of rewards.

Conditional withholding of proboscis extension in honeybees (Apis mellifera) during discriminative punishment.

PubMed

Smith, B H; Abramson, C I; Tobin, T R

1991-12-01

Proboscis extension conditioning of honeybee workers was used to test the ability of bees to respond to appetitive and aversive stimuli while restrained in a harness that allows subjects to move their antennae and mouthparts (Kuwabara, 1957; Menzel, Erber, & Masuhr, 1974). Subjects were conditioned to discriminate between two odors, one associated with sucrose feeding and the other associated with a 10 V AC shock if they responded to the sucrose unconditioned stimulus (US) in the context of that odor. Most Ss readily learned to respond to the odor followed by sucrose feeding and not to the odor associated with sucrose stimulation plus shock. Furthermore, in the context of the odor associated with shock, significantly more subjects withheld or delayed proboscis extension on stimulation with the sucrose US than they did in the context of the odor associated with feeding. Thus, restrained honeybees can readily learn to avoid shock according to an odor context by withholding proboscis extension to a normally powerful releaser. Analysis of individual learning curves revealed that subjects differed markedly in performance on this task. Some learn the discrimination quickly, whereas others show different kinds of response patterns.

49 CFR 195.432 - Inspection of in-service breakout tanks.

Code of Federal Regulations, 2014 CFR

2014-10-01

... low-pressure steel aboveground breakout tanks according to API Standard 653 (incorporated by reference... breakout tanks built to API Standard 2510 according to section 6 of API 510. (d) The intervals of...

49 CFR 195.432 - Inspection of in-service breakout tanks.

Code of Federal Regulations, 2012 CFR

2012-10-01

... low-pressure steel aboveground breakout tanks according to API Standard 653 (incorporated by reference... breakout tanks built to API Standard 2510 according to section 6 of API 510. (d) The intervals of...

49 CFR 195.432 - Inspection of in-service breakout tanks.

Code of Federal Regulations, 2011 CFR

2011-10-01

... low-pressure steel aboveground breakout tanks according to API Standard 653 (incorporated by reference... breakout tanks built to API Standard 2510 according to section 6 of API 510. (d) The intervals of...

49 CFR 195.432 - Inspection of in-service breakout tanks.

Code of Federal Regulations, 2010 CFR

2010-10-01

... low-pressure steel aboveground breakout tanks according to API Standard 653 (incorporated by reference... breakout tanks built to API Standard 2510 according to section 6 of API 510. (d) The intervals of...

49 CFR 195.432 - Inspection of in-service breakout tanks.

Code of Federal Regulations, 2013 CFR

2013-10-01

... low-pressure steel aboveground breakout tanks according to API Standard 653 (incorporated by reference... breakout tanks built to API Standard 2510 according to section 6 of API 510. (d) The intervals of...

Infections with the Sexually Transmitted Pathogen Nosema apis Trigger an Immune Response in the Seminal Fluid of Honey Bees (Apis mellifera).

PubMed

Grassl, Julia; Peng, Yan; Baer-Imhoof, Barbara; Welch, Mat; Millar, A Harvey; Baer, Boris

2017-01-06

Honey bee (Apis mellifera) males are highly susceptible to infections with the sexually transmitted fungal pathogen Nosema apis. However, they are able to suppress this parasite in the ejaculate using immune molecules in the seminal fluid. We predicted that males respond to infections by altering the seminal fluid proteome to minimize the risk to sexually transmit the parasite to the queen and her colony. We used iTRAQ isotopic labeling to compare seminal fluid proteins from infected and noninfected males and found that N. apis infections resulted in significant abundance changes in 111 of the 260 seminal fluid proteins quantitated. The largest group of proteins with significantly changed abundances consisted of 15 proteins with well-known immune-related functions, which included two significantly more abundant chitinases in the seminal fluid of infected males. Chitinases were previously hypothesized to be involved in honey bee antifungal activity against N. apis. Here we show that infection with N. apis triggers a highly specific immune response in the seminal fluid of honey bee males.

Hot-stage microscopy for determination of API particles in a formulated tablet.

PubMed

Simek, Michal; Grünwaldová, Veronika; Kratochvíl, Bohumil

2014-01-01

Although methods exist to readily determine the particle size distribution (PSD) of an active pharmaceutical ingredient (API) before its formulation into a final product, the primary challenge is to develop a method to determine the PSD of APIs in a finished tablet. To address the limitations of existing PSD methods, we used hot-stage microscopy to observe tablet disintegration during temperature change and, thus, reveal the API particles in a tablet. Both mechanical and liquid disintegration were evaluated after we had identified optimum milling time for mechanical disintegration and optimum volume of water for liquid disintegration. In each case, hot-stage micrographs, taken before and after the API melting point, were compared with image analysis software to obtain the PSDs. Then, the PSDs of the APIs from the disintegrated tablets were compared with the PSDs of raw APIs. Good agreement was obtained, thereby confirming the robustness of our methodology. The availability of such a method equips pharmaceutical scientists with an in vitro assessment method that will more reliably determine the PSD of active substances in finished tablets.

GIANT API: an application programming interface for functional genomics.

PubMed

Roberts, Andrew M; Wong, Aaron K; Fisk, Ian; Troyanskaya, Olga G

2016-07-08

GIANT API provides biomedical researchers programmatic access to tissue-specific and global networks in humans and model organisms, and associated tools, which includes functional re-prioritization of existing genome-wide association study (GWAS) data. Using tissue-specific interaction networks, researchers are able to predict relationships between genes specific to a tissue or cell lineage, identify the changing roles of genes across tissues and uncover disease-gene associations. Additionally, GIANT API enables computational tools like NetWAS, which leverages tissue-specific networks for re-prioritization of GWAS results. The web services covered by the API include 144 tissue-specific functional gene networks in human, global functional networks for human and six common model organisms and the NetWAS method. GIANT API conforms to the REST architecture, which makes it stateless, cacheable and highly scalable. It can be used by a diverse range of clients including web browsers, command terminals, programming languages and standalone apps for data analysis and visualization. The API is freely available for use at http://giant-api.princeton.edu. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Novel medium-throughput technique for investigating drug-cyclodextrin complexation by pH-metric titration using the partition coefficient method.

PubMed

Dargó, Gergő; Boros, Krisztina; Péter, László; Malanga, Milo; Sohajda, Tamás; Szente, Lajos; Balogh, György T

2018-05-05

The present study was aimed to develop a medium-throughput screening technique for investigation of cyclodextrin (CD)-active pharmaceutical ingredient (API) complexes. Dual-phase potentiometric lipophilicity measurement, as gold standard technique, was combined with the partition coefficient method (plotting the reciprocal of partition coefficients of APIs as a function of CD concentration). A general equation was derived for determination of stability constants of 1:1 CD-API complexes (K 1:1,CD ) based on solely the changes of partition coefficients (logP o/w N -logP app N ), without measurement of the actual API concentrations. Experimentally determined logP value (-1.64) of 6-deoxy-6[(5/6)-fluoresceinylthioureido]-HPBCD (FITC-NH-HPBCD) was used to estimate the logP value (≈ -2.5 to -3) of (2-hydroxypropyl)-ß-cyclodextrin (HPBCD). The results suggested that the amount of HPBCD can be considered to be inconsequential in the octanol phase. The decrease of octanol volume due to the octanol-CD complexation was considered, thus a corrected octanol-water phase ratio was also introduced. The K 1:1,CD values obtained by this developed method showed a good accordance with the results from other orthogonal methods. Copyright © 2018 Elsevier B.V. All rights reserved.

Highly sensitive screening method for nitroaromatic, nitramine and nitrate ester explosives by high performance liquid chromatography-atmospheric pressure ionization-mass spectrometry (HPLC-API-MS) in forensic applications.

PubMed

Xu, Xiaoma; van de Craats, Anick M; de Bruyn, Peter C A M

2004-11-01

A highly sensitive screening method based on high performance liquid chromatography atmospheric pressure ionization mass spectrometry (HPLC-API-MS) has been developed for the analysis of 21 nitroaromatic, nitramine and nitrate ester explosives, which include the explosives most commonly encountered in forensic science. Two atmospheric pressure ionization (API) methods, atmospheric pressure chemical ionization (APCI) and electrospray ionization (ESI), and various experimental conditions have been applied to allow for the detection of all 21 explosive compounds. The limit of detection (LOD) in the full-scan mode has been found to be 0.012-1.2 ng on column for the screening of most explosives investigated. For nitrobenzene, an LOD of 10 ng was found with the APCI method in the negative mode. Although the detection of nitrobenzene, 2-, 3-, and 4-nitrotoluene is hindered by the difficult ionization of these compounds, we have found that by forming an adduct with glycine, LOD values in the range of 3-16 ng on column can be achieved. Compared with previous screening methods with thermospray ionization, the API method has distinct advantages, including simplicity and stability of the method applied, an extended screening range and a low detection limit for the explosives studied.

Heterogeneous scalable framework for multiphase flows

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

Morris, Karla Vanessa

2013-09-01

Two categories of challenges confront the developer of computational spray models: those related to the computation and those related to the physics. Regarding the computation, the trend towards heterogeneous, multi- and many-core platforms will require considerable re-engineering of codes written for the current supercomputing platforms. Regarding the physics, accurate methods for transferring mass, momentum and energy from the dispersed phase onto the carrier fluid grid have so far eluded modelers. Significant challenges also lie at the intersection between these two categories. To be competitive, any physics model must be expressible in a parallel algorithm that performs well on evolving computermore » platforms. This work created an application based on a software architecture where the physics and software concerns are separated in a way that adds flexibility to both. The develop spray-tracking package includes an application programming interface (API) that abstracts away the platform-dependent parallelization concerns, enabling the scientific programmer to write serial code that the API resolves into parallel processes and threads of execution. The project also developed the infrastructure required to provide similar APIs to other application. The API allow object-oriented Fortran applications direct interaction with Trilinos to support memory management of distributed objects in central processing units (CPU) and graphic processing units (GPU) nodes for applications using C++.« less

APIS : an interactive database of HST-UV observations of the outer planets

NASA Astrophysics Data System (ADS)

Lamy, Laurent; Henry, Florence; Prangé, Renée; Le Sidaner, Pierre

2014-05-01

Remote UV measurement of the outer planets offer a wealth of informations on rings, moons, planetary atmospheres and magnetospheres. Auroral emissions in particular provide highly valuable constraints on the auroral processes at work and the underlying coupling between the solar wind, the magnetosphere, the ionosphere and the moons. Key observables provided by high resolution spectro-imaging include the spatial topology and the dynamics of active magnetic field lines, the radiated and the precipitated powers or the energy of precipitating particles. The Hubble Space Telescope (HST) acquired thousands of Far-UV spectra and images of the aurorae of Jupiter, Saturn and Uranus since 1993, feeding in numerous magnetospheric studies. But their use remains generally limited, owing to the difficulty to access and use raw and value-added data. APIS, the egyptian god of fertilization, is also the acronym of a new database (Auroral Planetary Imaging and Spectroscopy), aimed at facilitating the use of HST planetary auroral observations. APIS is based at the Virtual Observatory (VO) of Paris and provides a free and interactive access to a variety of high level data through a simple research interface and standard VO tools (as Aladin, Specview). We will present the capabilities of APIS and illustrate them with several examples.

APIS : an interactive database of HST-UV observations of the outer planets

NASA Astrophysics Data System (ADS)

Lamy, L.; Henry, F.; Prangé, R.; Le Sidaner, P.

2013-09-01

Remote UV measurement of the outer planets are a wealth of informations on rings, moons, planetary atmospheres and magnetospheres. Auroral emissions in particular provide highly valuable constraints on the auroral processes at work and the underlying coupling between the solar wind, the magnetosphere, the ionosphere and the moons. Key observables provided by high resolution spectro-imaging include the spatial topology and the dynamics of active magnetic field lines, the radiated and the precipitated powers or the energy of precipitating particles. The Hubble Space Telescope (HST) acquired thousands of Far-UV spectra and images of the aurorae of Jupiter, Saturn and Uranus since 1993, feeding in numerous magnetospheric studies. But their use remains generally limited, owing to the difficulty to access and use raw and value-added data. APIS, the egyptian god of fertilization, is also the acronym of a new database (Auroral Planetary Imaging and Spectroscopy, Figure 1), aimed at facilitating the use of HST planetary auroral observations. APIS is based at the Virtual Observatory (VO) of Paris and provides a free and interactive access to a variety of high level data through a simple research interface and standard VO tools. We will present the capabilities of APIS and illustrate them with several examples.

The Value of Pre-Screening in the Alzheimer’s Prevention Initiative (API) Autosomal Dominant Alzheimer’s Disease Trial

PubMed Central

Rios-Romenets, S.; Giraldo-Chica, M.; López, H.; Piedrahita, F.; Ramos, C.; Acosta-Baena, N.; Muñoz, C.; Ospina, P.; Tobón, C.; Cho, W.; Ward, M.; Langbaum, J.B.; Tariot, P.N.; Reiman, E.M.; Lopera, F.

2018-01-01

The Alzheimer’s Prevention Initiative (API) Autosomal Dominant Alzheimer’s Disease (ADAD) trial evaluates the anti-amyloid-β antibody crenezumab in cognitively unimpaired persons who, based on genetic background and age, are at high imminent risk of clinical progression, and provides a powerful test of the amyloid hypothesis. The Neurosciences Group of Antioquia implemented a pre-screening process with the goals of decreasing screen failures and identifying participants most likely to adhere to trial requirements of the API ADAD trial in cognitively unimpaired members of Presenilin1 E280A mutation kindreds. The pre-screening failure rate was 48.2%: the primary reason was expected inability to comply with the protocol, chiefly due to work requirements. More carriers compared to non-carriers, and more males compared to females, failed pre-screening. Carriers with illiteracy or learning/comprehension difficulties failed pre-screening more than non-carriers. With the Colombian API Registry and our prescreening efforts, we randomized 169 30–60 year-old cognitively unimpaired carriers and 83 non-carriers who agreed to participate in the trial for at least 60 months. Our findings suggest multiple benefits of implementing a pre-screening process for enrolling prevention trials in ADAD. PMID:29405233

BEAGLE: an application programming interface and high-performance computing library for statistical phylogenetics.

PubMed

Ayres, Daniel L; Darling, Aaron; Zwickl, Derrick J; Beerli, Peter; Holder, Mark T; Lewis, Paul O; Huelsenbeck, John P; Ronquist, Fredrik; Swofford, David L; Cummings, Michael P; Rambaut, Andrew; Suchard, Marc A

2012-01-01

Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software.

BEAGLE: An Application Programming Interface and High-Performance Computing Library for Statistical Phylogenetics

PubMed Central

Ayres, Daniel L.; Darling, Aaron; Zwickl, Derrick J.; Beerli, Peter; Holder, Mark T.; Lewis, Paul O.; Huelsenbeck, John P.; Ronquist, Fredrik; Swofford, David L.; Cummings, Michael P.; Rambaut, Andrew; Suchard, Marc A.

2012-01-01

Abstract Phylogenetic inference is fundamental to our understanding of most aspects of the origin and evolution of life, and in recent years, there has been a concentration of interest in statistical approaches such as Bayesian inference and maximum likelihood estimation. Yet, for large data sets and realistic or interesting models of evolution, these approaches remain computationally demanding. High-throughput sequencing can yield data for thousands of taxa, but scaling to such problems using serial computing often necessitates the use of nonstatistical or approximate approaches. The recent emergence of graphics processing units (GPUs) provides an opportunity to leverage their excellent floating-point computational performance to accelerate statistical phylogenetic inference. A specialized library for phylogenetic calculation would allow existing software packages to make more effective use of available computer hardware, including GPUs. Adoption of a common library would also make it easier for other emerging computing architectures, such as field programmable gate arrays, to be used in the future. We present BEAGLE, an application programming interface (API) and library for high-performance statistical phylogenetic inference. The API provides a uniform interface for performing phylogenetic likelihood calculations on a variety of compute hardware platforms. The library includes a set of efficient implementations and can currently exploit hardware including GPUs using NVIDIA CUDA, central processing units (CPUs) with Streaming SIMD Extensions and related processor supplementary instruction sets, and multicore CPUs via OpenMP. To demonstrate the advantages of a common API, we have incorporated the library into several popular phylogenetic software packages. The BEAGLE library is free open source software licensed under the Lesser GPL and available from http://beagle-lib.googlecode.com. An example client program is available as public domain software. PMID:21963610

Source characterization of nervous system active pharmaceutical ingredients in healthcare wastewaters

EPA Science Inventory

Nervous system active pharmaceutical ingredients (APIs), including anti-depressants and opioids, are important clinically administered pharmaceuticals within healthcare facilities. Concentrations and mass loadings of ten nervous system APIs and three nervous system API metaboli...

[Effect of habitat and interspecific competition on Apis cerana cerana colony distribution].

PubMed

Yu, Linsheng; Han, Shengming

2003-04-01

Habitat change and interspecific competition were the main factors affecting, Apis cerana cerana colony distribution among Wannan and Wanxi Dabie mountainous areas, Jianghuai area and Huaibei plain. Wannan and Wanxi Dabie mountainous areas were the ideal places for Apis cerana cerana' habitation and propogation, in which, there were integrated natural vegetation, fine ecological condition, abundant nectariferous plants, and Apis cerana cerana had large colony size, wide distribution, high density, no disturbances of natural mating, and was dominant interspecific competition. In Jianghuai area and Huaibei plain, there were small covering of natural vegetation, different degree of degradation of ecological balance, few kinds of nectariferous plants with almost the same blooming periods, natural mating perturbed by Apis mellifera ligustica for Apis cerana cerana, and which was inferior in interspecific competition, colony size sharply decreased, distribution area reduced, and density cut down to a great extent. In Huaibei plain, the negative factors were more conspicuous.

Testing an Irrigation Decision Support Tool for California Specialty Crops

NASA Astrophysics Data System (ADS)

Johnson, L.; Cahn, M.; Benzen, S.; Zaragoza, I.; Murphy, L.; Melton, F. S.; Martin, F.; Quackenbush, A.; Lockhart, T.

2015-12-01

Estimation of crop evapotranspiration supports efficiency of irrigation water management, which in turn can mitigate nitrate leaching, groundwater depletion, and provide energy savings. Past research in California and elsewhere has revealed strong relationships between photosynthetically active vegetation fraction (Fc) and crop evapotranspiration (ETc). Additional research has shown the potential of monitoring Fc by satellite remote sensing. The U.C. Cooperative Extension developed and operates CropManage (CM) as on-line database irrigation (and nitrogen) scheduling tool. CM accounts for the rapid growth and typically brief cycle of cool-season vegetables, where Fc and fraction of reference ET can change daily during canopy development. The model automates crop water requirement calculations based on reference ET data collected by California Dept. Water Resources. Empirically-derived equations are used to estimate daily Fc time-series for a given crop type primarily as a function of planting date and expected harvest date. An application programming interface (API) is under development to provide a check on modeled Fc of current crops and facilitate CM expansion to new crops. The API will enable CM to extract field scale Fc observations from NASA's Satellite Irrigation Management Support (SIMS). SIMS is mainly Landsat based and currently monitors Fc over about 8 million irrigation acres statewide, with potential for adding data from ESA/Sentinel for improved temporal resolution. In the current study, a replicated irrigation trial was performed on romaine lettuce at the USDA Agricultural Research Station in Salinas, CA. CropManage recommendations were used to guide water treatments by drip irrigation at 50%, 75%, 100% ETc replacement levels, with an added treatment at 150% ET representing grower standard practice. Experimental results indicate that yields from the 100% and 150% treatments were not significantly different and were in-line with industry average, while yields from the 75% and 50% treatments were significantly lower. Additional results will be presented with respect to a subsequent cabbage trial harvested October 2015.

Review of oil families and their petroleum systems of the Williston Basin

USGS Publications Warehouse

Lillis, Paul G.

2013-01-01

Oil bulk properties such as API gravity, sulfur content, and pour point are much underutilized in the recent geochemical literature and are found to be useful here in differentiating oil families. The Red River petroleum system has two oil families that can be differentiated based on pour point. The oils in the Madison petroleum system can be divided into two families based on API gravity-sulfur content relationships, with one family derived from Type II-S kerogen and the other family derived from Type II kerogen with medium sulfur content. The Tyler petroleum system of the Williston Basin may be distinguished from the Heath-Tyler petroleum system in central Montana based on differences in geology and petroleum geochemistry, with Tyler petroleum system oils having a higher pour point and lower sulfur content.

Infectivity and virulence of Nosema ceranae and Nosema apis in commercially available North American honey bees.

PubMed

Huang, Wei-Fone; Solter, Leellen; Aronstein, Katherine; Huang, Zachary

2015-01-01

Nosema ceranae infection is ubiquitous in western honey bees, Apis mellifera, in the United States and the pathogen has apparently replaced Nosema apis in colonies nationwide. Displacement of N. apis suggests that N. ceranae has competitive advantages but N. ceranae was significantly less infective and less virulent than N. apis in commercially available lineages of honey bees in studies conducted in Illinois and Texas. At 5 days post eclosion, the most susceptible age of adult bees tested, the mean ID50 for N. apis was 359 spores compared to 3217 N. ceranae spores, a nearly 9-fold difference. Infectivity of N. ceranae was also lower than N. apis for 24-h and 14-day worker bees. N. ceranae was less infective than reported in studies using European strains of honey bees, while N. apis infectivity, tested in the same cohort of honey bees, corresponded to results reported globally from 1972 to 2010. Mortality of worker bees was similar for both pathogens at a dosage of 50 spores and was not different from the uninfected controls, but was significantly higher for N. apis than N. ceranae at dosages ⩾500 spores. Our results provide comparisons for evaluating research using different ages of bees and pathogen dosages and clarify some controversies. In addition, comparisons among studies suggest that the mixed lineages of US honey bees may be less susceptible to N. ceranae infections than are European bees or that the US isolates of the pathogen are less infective and less virulent than European isolates. Copyright © 2014 Elsevier Inc. All rights reserved.

Cloning, expression pattern, and potential role of apoptosis inhibitor 5 in the termination of embryonic diapause and early embryo development of Artemia sinica.

PubMed

Zhang, Shuang; Yao, Feng; Jing, Ting; Zhang, Mengchen; Zhao, Wei; Zou, Xiangyang; Sui, Linlin; Hou, Lin

2017-09-10

During the embryonic development of Artemia sinica, the diapause phenomenon can be induced by high salinity or low temperature conditions. The diapause embryo at the gastrula stage is maintained under the threat of apoptosis to guarantee the embryo's normal development. In this process, apoptosis inhibitor proteins play vital roles in protecting embryos against apoptosis. Apoptosis inhibitor5 (API5) plays a pivotal role in regulating the cell cycle and preventing programmed cell death after growth factor starvation. In the present study, we cloned the full-length cDNA representing the api5 gene from A. sinica (As-api5), which encodes a 372-amino acid protein. In situ hybridization experiments revealed that As-api5 expression is not tissue or organ specific. Quantitative real-time PCR analyses of the developmental expression of As-api5 showed that it reached its highest level at 10h, after which its expression decreased. High salinity and low temperature treatments increased the expression of As-api5. Western blotting was used to assess the abundance of As-API5 and related proteins (As-CyclinA, As-CyclinE, As-E2F1, As-CDK2, As-APAF1, and As-Caspase9). Downregulation of As-api5 expression using a short interfering RNA resulted in increased mortality and embryo malformation of A. sinica. Taken together, the results indicated that API5 plays a crucial role in embryonic diapause termination and early embryo development of A. sinica. Copyright © 2017. Published by Elsevier B.V.

Api m 10, a genuine A. mellifera venom allergen, is clinically relevant but underrepresented in therapeutic extracts.

PubMed

Blank, S; Seismann, H; Michel, Y; McIntyre, M; Cifuentes, L; Braren, I; Grunwald, T; Darsow, U; Ring, J; Bredehorst, R; Ollert, M; Spillner, E

2011-10-01

Generalized systemic reactions to stinging hymenoptera venom constitute a potentially fatal condition in venom-allergic individuals. Hence, the identification and characterization of all allergens is imperative for improvement of diagnosis and design of effective immunotherapeutic approaches. Our aim was the immunochemical characterization of the carbohydrate-rich protein Api m 10, an Apis mellifera venom component and putative allergen, with focus on the relevance of glycosylation. Furthermore, the presence of Api m 10 in honeybee venom (HBV) and licensed venom immunotherapy preparations was addressed. Api m 10 was produced as soluble, aglycosylated protein in Escherichia coli and as differentially glycosylated protein providing a varying degree of fucosylation in insect cells. IgE reactivity and basophil activation of allergic patients were analyzed. For detection of Api m 10 in different venom preparations, a monoclonal human IgE antibody was generated. Both, the aglycosylated and the glycosylated variant of Api m 10 devoid of cross-reactive carbohydrate determinants (CCD), exhibited IgE reactivity with approximately 50% of HBV-sensitized patients. A corresponding reactivity could be documented for the activation of basophils. Although the detection of the native protein in crude HBV suggested content comparable to other relevant allergens, three therapeutical HBV extracts lacked detectable amounts of this component. Api m 10 is a genuine allergen of A. mellifera venom with IgE sensitizing potential in a significant fraction of allergic patients independent of CCD reactivity. Thus, Api m 10 could become a key element for component-resolved diagnostic tests and improved immunotherapeutic approaches in hymenoptera venom allergy. © 2011 John Wiley & Sons A/S.

Spatial-Temporal Analysis of Air Pollution, Climate Change, and Total Mortality in 120 Cities of China, 2012-2013.

PubMed

Liu, Longjian; Yang, Xuan; Liu, Hui; Wang, Mingquan; Welles, Seth; Márquez, Shannon; Frank, Arthur; Haas, Charles N

2016-01-01

China has had a rapid increase in its economy over the past three decades. However, the economic boom came at a certain cost of depleting air quality. In the study, we aimed to examine the burden of air pollution and its association with climatic factors and health outcomes using data from Chinese national and city-level air quality and public health surveillance systems. City-level daily air pollution index (API, a sum weighted index of SO2, NO2, PM10, CO, and Ozone) in 120 cities in 2012 and 2013, and its association with climate factors were analyzed using multiple linear regression analysis, spatial autocorrelation analysis, and panel fixed models. City-level ecological association between annual average API and total mortality were examined using univariate and partial correlation analysis. Sensitivity analysis was conducted by taking the consideration of time-lag effect between exposures and outcomes. The results show that among the 120 cities, annual average API significantly increased from 2012 to 2013 (65.05 vs. 75.99, p < 0.0001). The highest average API was in winter, and the lowest in summer. A significantly spatial clustering of elevated API was observed, with the highest API in northwest China in 2012 and with the highest in east China in 2013. In 2012, 5 (4%) of the 120 cities had ≥60 days with API >100 (defined as "slightly polluted"), however, it increased to 21 cities (18%) that experienced API >100 for ≥60 days in 2013. Furthermore, 16 cities (13%) in 2012 and 35 (29%) in 2013 experienced a maximum API >300 (defined as "severely polluted"). API was negatively and significantly correlated with heat index, precipitation, and sunshine hours, but positively with air pressure. Cities with higher API concentrations had significantly higher total mortality rates than those with lower API. About a 4-7% of the variation in total mortality could be explained by the difference in API across the nation. In conclusion, the study highlights an increased trend of air pollution from 2012 to 2013 in China. The magnitude of air pollution varied by seasons and regions and correlated with climatic factors and total mortality across the country.

Spatial–Temporal Analysis of Air Pollution, Climate Change, and Total Mortality in 120 Cities of China, 2012–2013

PubMed Central

Liu, Longjian; Yang, Xuan; Liu, Hui; Wang, Mingquan; Welles, Seth; Márquez, Shannon; Frank, Arthur; Haas, Charles N.

2016-01-01

China has had a rapid increase in its economy over the past three decades. However, the economic boom came at a certain cost of depleting air quality. In the study, we aimed to examine the burden of air pollution and its association with climatic factors and health outcomes using data from Chinese national and city-level air quality and public health surveillance systems. City-level daily air pollution index (API, a sum weighted index of SO2, NO2, PM10, CO, and Ozone) in 120 cities in 2012 and 2013, and its association with climate factors were analyzed using multiple linear regression analysis, spatial autocorrelation analysis, and panel fixed models. City-level ecological association between annual average API and total mortality were examined using univariate and partial correlation analysis. Sensitivity analysis was conducted by taking the consideration of time-lag effect between exposures and outcomes. The results show that among the 120 cities, annual average API significantly increased from 2012 to 2013 (65.05 vs. 75.99, p < 0.0001). The highest average API was in winter, and the lowest in summer. A significantly spatial clustering of elevated API was observed, with the highest API in northwest China in 2012 and with the highest in east China in 2013. In 2012, 5 (4%) of the 120 cities had ≥60 days with API >100 (defined as “slightly polluted”), however, it increased to 21 cities (18%) that experienced API >100 for ≥60 days in 2013. Furthermore, 16 cities (13%) in 2012 and 35 (29%) in 2013 experienced a maximum API >300 (defined as “severely polluted”). API was negatively and significantly correlated with heat index, precipitation, and sunshine hours, but positively with air pressure. Cities with higher API concentrations had significantly higher total mortality rates than those with lower API. About a 4–7% of the variation in total mortality could be explained by the difference in API across the nation. In conclusion, the study highlights an increased trend of air pollution from 2012 to 2013 in China. The magnitude of air pollution varied by seasons and regions and correlated with climatic factors and total mortality across the country. PMID:27486572

EnergyPlus Graphical User Interface

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

2011-01-04

LBNL, Infosys Technologies and Digital Alchemy are developing a free, comprehensive graphical user interface (GUI) that will enable EnergyPlus to be used more easily and effectively by building designers and other professionals, facilitating its widespread adoption. User requirements have been defined through a series of practitioner workshops. A new schematic editor for HVAC systems will be combined with different building envelope geometry generation tools and IFC-based BIM import and export. LBNL and Digital Alchemy have generated a detailed function requirements specification, which is being implemented in software by Infosys, LBNL and and Digital Alchemy. LBNL and practitioner subcontractors will developmore » a comprehensive set of templates and libraries and will perform extensive testing of the GUI before it is released in Q3 2011. It is planned to use an Open Platfom approach, in which a comprehensive set of well documented Application Programming Interfaces (API's) would be provided to facilitate both the development of third party contributions to the official, standard GUI and the development of derivative works.« less

Genomic region operation kit for flexible processing of deep sequencing data.

PubMed

Ovaska, Kristian; Lyly, Lauri; Sahu, Biswajyoti; Jänne, Olli A; Hautaniemi, Sampsa

2013-01-01

Computational analysis of data produced in deep sequencing (DS) experiments is challenging due to large data volumes and requirements for flexible analysis approaches. Here, we present a mathematical formalism based on set algebra for frequently performed operations in DS data analysis to facilitate translation of biomedical research questions to language amenable for computational analysis. With the help of this formalism, we implemented the Genomic Region Operation Kit (GROK), which supports various DS-related operations such as preprocessing, filtering, file conversion, and sample comparison. GROK provides high-level interfaces for R, Python, Lua, and command line, as well as an extension C++ API. It supports major genomic file formats and allows storing custom genomic regions in efficient data structures such as red-black trees and SQL databases. To demonstrate the utility of GROK, we have characterized the roles of two major transcription factors (TFs) in prostate cancer using data from 10 DS experiments. GROK is freely available with a user guide from >http://csbi.ltdk.helsinki.fi/grok/.

Pharmaceutical Cocrystals: New Solid Phase Modification Approaches for the Formulation of APIs.

PubMed

Karagianni, Anna; Malamatari, Maria; Kachrimanis, Kyriakos

2018-01-25

Cocrystals can be used as an alternative approach based on crystal engineering to enhance specific physicochemical and biopharmaceutical properties of active pharmaceutical ingredients (APIs) when the approaches to salt or polymorph formation do not meet the expected targets. In this article, an overview of pharmaceutical cocrystals will be presented, with an emphasis on the intermolecular interactions in cocrystals and the methods for their preparation. Furthermore, cocrystals of direct pharmaceutical interest, along with their in vitro properties and available in vivo data and characterization techniques are discussed, highlighting the potential of cocrystals as an attractive route for drug development.

Reduced SNP Panels for Genetic Identification and Introgression Analysis in the Dark Honey Bee (Apis mellifera mellifera)

PubMed Central

Muñoz, Irene; Henriques, Dora; Johnston, J. Spencer; Chávez-Galarza, Julio; Kryger, Per; Pinto, M. Alice

2015-01-01

Beekeeping activities, especially queen trading, have shaped the distribution of honey bee (Apis mellifera) subspecies in Europe, and have resulted in extensive introductions of two eastern European C-lineage subspecies (A. m. ligustica and A. m. carnica) into the native range of the M-lineage A. m. mellifera subspecies in Western Europe. As a consequence, replacement and gene flow between native and commercial populations have occurred at varying levels across western European populations. Genetic identification and introgression analysis using molecular markers is an important tool for management and conservation of honey bee subspecies. Previous studies have monitored introgression by using microsatellite, PCR-RFLP markers and most recently, high density assays using single nucleotide polymorphism (SNP) markers. While the latter are almost prohibitively expensive, the information gained to date can be exploited to create a reduced panel containing the most ancestry-informative markers (AIMs) for those purposes with very little loss of information. The objective of this study was to design reduced panels of AIMs to verify the origin of A. m. mellifera individuals and to provide accurate estimates of the level of C-lineage introgression into their genome. The discriminant power of the SNPs using a variety of metrics and approaches including the Weir & Cockerham’s FST, an FST-based outlier test, Delta, informativeness (In), and PCA was evaluated. This study shows that reduced AIMs panels assign individuals to the correct origin and calculates the admixture level with a high degree of accuracy. These panels provide an essential tool in Europe for genetic stock identification and estimation of admixture levels which can assist management strategies and monitor honey bee conservation programs. PMID:25875986

Volcanic Ash and Aviation - the 2014 Eruptions of Kelut and Sangeang Api, Indonesia

NASA Astrophysics Data System (ADS)

Tupper, A. C.; Jansons, E.

2014-12-01

Two significant eruptions in Indonesia during the first part of 2014 have highlighted the continuing challenges of safe air traffic management around volcanic ash clouds. The stratospheric eruption of Kelut (also known as Kelud) in Java late on 13 February 2014 resulted in widespread aviation disruption over Indonesia and at least one serious volcanic ash encounter from an international airline. An upper-tropospheric eruption of Sangeang Api in the Lesser Sunda Islands on 30 May 2014 did not result in any known aircraft encounters, but did result in many delays and flight cancellations between Indonesia and Australia. In both cases, the eruption and resultant ash clouds were relatively well observed, if subject to the usual issues in characterising such clouds. For example, as tropical eruptions frequently reach 15 km amsl and above due to the height of the tropical tropopause, it is frequently very difficult to provide an accurate estimation of conditions at the cruising levels of aircraft, at 10-11 km (or lower for shorter domestic routes). More critically, the challenge of linking operational results from two scientific professions (volcanology and meteorology) with real-time aviation users remains strongly evident. Situational awareness of domestic and international airlines, ground-based monitoring and communications prior to and during the eruption, receiving and sharing pilot reports of volcanic ash, and appropriate flight responses all remain inadequate even in relatively fine conditions, with an unacceptable ongoing risk of serious aviation encounters should improvements not be made. Despite the extensive efforts of the International Civil Aviation Organization, World Meteorological Organization, and all partners in the International Airways Volcano Watch, and despite the acceleration of work on the issue since 2010, volcanic ash management remains sub-optimal.

Assessment of powder blend uniformity: Comparison of real-time NIR blend monitoring with stratified sampling in combination with HPLC and at-line NIR Chemical Imaging.

PubMed

Bakri, Barbara; Weimer, Marco; Hauck, Gerrit; Reich, Gabriele

2015-11-01

Scope of the study was (1) to develop a lean quantitative calibration for real-time near-infrared (NIR) blend monitoring, which meets the requirements in early development of pharmaceutical products and (2) to compare the prediction performance of this approach with the results obtained from stratified sampling using a sample thief in combination with off-line high pressure liquid chromatography (HPLC) and at-line near-infrared chemical imaging (NIRCI). Tablets were manufactured from powder blends and analyzed with NIRCI and HPLC to verify the real-time results. The model formulation contained 25% w/w naproxen as a cohesive active pharmaceutical ingredient (API), microcrystalline cellulose and croscarmellose sodium as cohesive excipients and free-flowing mannitol. Five in-line NIR calibration approaches, all using the spectra from the end of the blending process as reference for PLS modeling, were compared in terms of selectivity, precision, prediction accuracy and robustness. High selectivity could be achieved with a "reduced" approach i.e. API and time saving approach (35% reduction of API amount) based on six concentration levels of the API with three levels realized by three independent powder blends and the additional levels obtained by simply increasing the API concentration in these blends. Accuracy and robustness were further improved by combining this calibration set with a second independent data set comprising different excipient concentrations and reflecting different environmental conditions. The combined calibration model was used to monitor the blending process of independent batches. For this model formulation the target concentration of the API could be achieved within 3 min indicating a short blending time. The in-line NIR approach was verified by stratified sampling HPLC and NIRCI results. All three methods revealed comparable results regarding blend end point determination. Differences in both mean API concentration and RSD values could be attributed to differences in effective sample size and thief sampling errors. This conclusion was supported by HPLC and NIRCI analysis of tablets manufactured from powder blends after different blending times. In summary, the study clearly demonstrates the ability to develop efficient and robust quantitative calibrations for real-time NIR powder blend monitoring with a reduced set of powder blends while avoiding any bias caused by physical sampling. Copyright © 2015 Elsevier B.V. All rights reserved.

The influence of uncertainty and location-specific conditions on the environmental prioritisation of human pharmaceuticals in Europe.

PubMed

Oldenkamp, Rik; Huijbregts, Mark A J; Ragas, Ad M J

2016-05-01

The selection of priority APIs (Active Pharmaceutical Ingredients) can benefit from a spatially explicit approach, since an API might exceed the threshold of environmental concern in one location, while staying below that same threshold in another. However, such a spatially explicit approach is relatively data intensive and subject to parameter uncertainty due to limited data. This raises the question to what extent a spatially explicit approach for the environmental prioritisation of APIs remains worthwhile when accounting for uncertainty in parameter settings. We show here that the inclusion of spatially explicit information enables a more efficient environmental prioritisation of APIs in Europe, compared with a non-spatial EU-wide approach, also under uncertain conditions. In a case study with nine antibiotics, uncertainty distributions of the PAF (Potentially Affected Fraction) of aquatic species were calculated in 100∗100km(2) environmental grid cells throughout Europe, and used for the selection of priority APIs. Two APIs have median PAF values that exceed a threshold PAF of 1% in at least one environmental grid cell in Europe, i.e., oxytetracycline and erythromycin. At a tenfold lower threshold PAF (i.e., 0.1%), two additional APIs would be selected, i.e., cefuroxime and ciprofloxacin. However, in 94% of the environmental grid cells in Europe, no APIs exceed either of the thresholds. This illustrates the advantage of following a location-specific approach in the prioritisation of APIs. This added value remains when accounting for uncertainty in parameter settings, i.e., if the 95th percentile of the PAF instead of its median value is compared with the threshold. In 96% of the environmental grid cells, the location-specific approach still enables a reduction of the selection of priority APIs of at least 50%, compared with a EU-wide prioritisation. Copyright © 2016 Elsevier Ltd. All rights reserved.

Automatic sampling and analysis of organics and biomolecules by capillary action-supported contactless atmospheric pressure ionization mass spectrometry.

PubMed

Hsieh, Cheng-Huan; Meher, Anil Kumar; Chen, Yu-Chie

2013-01-01

Contactless atmospheric pressure ionization (C-API) method has been recently developed for mass spectrometric analysis. A tapered capillary is used as both the sampling tube and spray emitter in C-API. No electric contact is required on the capillary tip during C-API mass spectrometric analysis. The simple design of the ionization method enables the automation of the C-API sampling system. In this study, we propose an automatic C-API sampling system consisting of a capillary (∼1 cm), an aluminium sample holder, and a movable XY stage for the mass spectrometric analysis of organics and biomolecules. The aluminium sample holder is controlled by the movable XY stage. The outlet of the C-API capillary is placed in front of the orifice of a mass spectrometer, whereas the sample well on the sample holder is moved underneath the capillary inlet. The sample droplet on the well can be readily infused into the C-API capillary through capillary action. When the sample solution reaches the capillary outlet, the sample spray is readily formed in the proximity of the mass spectrometer applied with a high electric field. The gas phase ions generated from the spray can be readily monitored by the mass spectrometer. We demonstrate that six samples can be analyzed in sequence within 3.5 min using this automatic C-API MS setup. Furthermore, the well containing the rinsing solvent is alternately arranged between the sample wells. Therefore, the C-API capillary could be readily flushed between runs. No carryover problems are observed during the analyses. The sample volume required for the C-API MS analysis is minimal, with less than 1 nL of the sample solution being sufficient for analysis. The feasibility of using this setup for quantitative analysis is also demonstrated.

Assessment of bitterness intensity and suppression effects using an Electronic Tongue

NASA Astrophysics Data System (ADS)

Legin, A.; Rudnitskaya, A.; Kirsanov, D.; Frolova, Yu.; Clapham, D.; Caricofe, R.

2009-05-01

Quantification of bitterness intensity and effectivness of bitterness suppression of a novel active pharmacological ingredient (API) being developed by GSK was performed using an Electronic Tongue (ET) based on potentiometric chemical sensors. Calibration of the ET was performed with solutions of quinine hydrochloride in the concentration range 0.4-360 mgL-1. An MLR calibration model was developed for predicting bitterness intensity expressed as "equivalent quinine concentration" of a series of solutions of quinine, bittrex and the API. Additionally the effectiveness of sucralose, mixture of aspartame and acesulfame K, and grape juice in masking the bitter taste of the API was assessed using two approaches. PCA models were produced and distances between compound containing solutions and corresponding placebos were calculated. The other approach consisted in calculating "equivalent quinine concentration" using a calibration model with respect to quinine concentration. According to both methods, the most effective taste masking was produced by grape juice, followed by the mixture of aspartame and acesulfame K.

G2S: a web-service for annotating genomic variants on 3D protein structures.

PubMed

Wang, Juexin; Sheridan, Robert; Sumer, S Onur; Schultz, Nikolaus; Xu, Dong; Gao, Jianjiong

2018-06-01

Accurately mapping and annotating genomic locations on 3D protein structures is a key step in structure-based analysis of genomic variants detected by recent large-scale sequencing efforts. There are several mapping resources currently available, but none of them provides a web API (Application Programming Interface) that supports programmatic access. We present G2S, a real-time web API that provides automated mapping of genomic variants on 3D protein structures. G2S can align genomic locations of variants, protein locations, or protein sequences to protein structures and retrieve the mapped residues from structures. G2S API uses REST-inspired design and it can be used by various clients such as web browsers, command terminals, programming languages and other bioinformatics tools for bringing 3D structures into genomic variant analysis. The webserver and source codes are freely available at https://g2s.genomenexus.org. g2s@genomenexus.org. Supplementary data are available at Bioinformatics online.

Infections of Nosema ceranae in four different honeybee species.

PubMed

Chaimanee, Veeranan; Warrit, Natapot; Chantawannakul, Panuwan

2010-10-01

The microsporidium Nosema ceranae is detected in honeybees in Thailand for the first time. This endoparasite has recently been reported to infect most Apis mellifera honeybee colonies in Europe, the US, and parts of Asia, and is suspected to have displaced the endemic endoparasite species, Nosema apis, from the western A. mellifera. We collected and identified species of microsporidia from the European honeybee (A. mellifera), the cavity nesting Asian honeybee (Apis cerana), the dwarf Asian honeybee (Apis florea) and the giant Asian honeybee (Apis dorsata) from colonies in Northern Thailand. We used multiplex PCR technique with two pairs of primers to differentiate N. ceranae from N. apis. From 80 A. mellifera samples, 62 (77.5%) were positively identified for the presence of the N. ceranae. Amongst 46 feral colonies of Asian honeybees (A. cerana, A. florea and A. dorsata) examined for Nosema infections, only N. ceranae could be detected. No N. apis was found in our samples. N. ceranae is found to be the only microsporidium infesting honeybees in Thailand. Moreover, we found the frequencies of N. ceranae infection in native bees to be less than that of A. mellifera. Copyright 2010 Elsevier Inc. All rights reserved.

Consequences of Nosema apis infection for male honey bees and their fertility

PubMed Central

Peng, Yan; Baer-Imhoof, Barbara; Harvey Millar, A.; Baer, Boris

2015-01-01

The queens of eusocial bees, ants and wasps mate only during a very short period early in life and males therefore produce ejaculates consisting of large numbers of high quality sperm. Such extreme selection for high fecundity resulted in males investing minimally into their somatic survival, including their immune system. However, if susceptible males are unable to protect their reproductive tissue from infections, they compromise queen fitness if they transfer pathogens during mating. We used the honey bee Apis mellifera and investigated the course of infection of the sexually transmitted pathogen Nosema apis. We predicted that honey bee males are susceptible but protect their reproductive tissues from infections. We investigated the effects of N. apis infections on the midgut, the accessory glands and the accessory testes and quantified the consequences of infection on male survival and fecundity. We found that N. apis is able to infect males, and as infections progressed, it significantly impacted fertility and survival in older males. Even though we confirm males to be able to minimize N. apis infections of their reproductive tissues, the parasite is present in ejaculates of older males. Consequently N. apis evolved alternative routes to successfully infect ejaculates and get sexually transmitted. PMID:26123530

Consequences of Nosema apis infection for male honey bees and their fertility.

PubMed

Peng, Yan; Baer-Imhoof, Barbara; Millar, A Harvey; Baer, Boris

2015-06-30

The queens of eusocial bees, ants and wasps mate only during a very short period early in life and males therefore produce ejaculates consisting of large numbers of high quality sperm. Such extreme selection for high fecundity resulted in males investing minimally into their somatic survival, including their immune system. However, if susceptible males are unable to protect their reproductive tissue from infections, they compromise queen fitness if they transfer pathogens during mating. We used the honey bee Apis mellifera and investigated the course of infection of the sexually transmitted pathogen Nosema apis. We predicted that honey bee males are susceptible but protect their reproductive tissues from infections. We investigated the effects of N. apis infections on the midgut, the accessory glands and the accessory testes and quantified the consequences of infection on male survival and fecundity. We found that N. apis is able to infect males, and as infections progressed, it significantly impacted fertility and survival in older males. Even though we confirm males to be able to minimize N. apis infections of their reproductive tissues, the parasite is present in ejaculates of older males. Consequently N. apis evolved alternative routes to successfully infect ejaculates and get sexually transmitted.

Acculturation and perceived stress in HIV+ immigrants: depression symptomatology in Asian and Pacific Islanders.

PubMed

Chen, Wei-Ti; Guthrie, Barbara; Shiu, Cheng-Shi; Yang, Joyce P; Weng, Zhongqi; Wang, Lixuan; Kamitani, Emiko; Fukuda, Yumiko; Luu, Binh Vinh

2014-01-01

Asians and Pacific Islanders (API) are among the fastest growing minority groups within the USA, and this growth has been accompanied by an increase in HIV incidence. Between 2000 and 2010, the API HIV infection rate increased from 4.5% to 8.7%; however, there is a paucity of HIV-related research for this group, and even less is known about the prevalence and correlates of antiretroviral therapy adherence behavior, quality of life, impact of stress, and efficacious self-management among HIV+ API Americans. This paper examines how acculturation and perceived stress affect depression symptomatology and treatment seeking in the HIV+ API population. A series of cross-sectional audio computer-assisted self-interviews were conducted with a convenience sample of 50 HIV+ API (29 in San Francisco and 21 in New York City). The relationship between acculturation and perceived stress was analyzed, and the results indicate that for those HIV+ API who reported low or moderate acculturation (as compared to those who reported high acculturation), stress was significantly mediated by depression symptomology. Interventions to address acculturation and reduce perceived stress among API generally and Asians specifically are therefore needed.

Understanding API-polymer proximities in amorphous stabilized composite drug products using fluorine-carbon 2D HETCOR solid-state NMR.

PubMed

Abraham, Anuji; Crull, George

2014-10-06

A simple and robust method for obtaining fluorine-carbon proximities was established using a (19)F-(13)C heteronuclear correlation (HETCOR) two-dimensional (2D) solid-state nuclear magnetic resonance (ssNMR) experiment under magic-angle spinning (MAS). The method was applied to study a crystalline active pharmaceutical ingredient (API), avagacestat, containing two types of fluorine atoms and its API-polymer composite drug product. These results provide insight into the molecular structure, aid with assigning the carbon resonances, and probe API-polymer proximities in amorphous spray dried dispersions (SDD). This method has an advantage over the commonly used (1)H-(13)C HETCOR because of the large chemical shift dispersion in the fluorine dimension. In the present study, fluorine-carbon distances up to 8 Å were probed, giving insight into the API structure, crystal packing, and assignments. Most importantly, the study demonstrates a method for probing an intimate molecular level contact between an amorphous API and a polymer in an SDD, giving insights into molecular association and understanding of the role of the polymer in API stability (such as recrystallization, degradation, etc.) in such novel composite drug products.

Prioritizing human pharmaceuticals for ecological risks in the freshwater environment of Korea.

PubMed

Ji, Kyunghee; Han, Eun Jeong; Back, Sunhyoung; Park, Jeongim; Ryu, Jisung; Choi, Kyungho

2016-04-01

Pharmaceutical residues are potential threats to aquatic ecosystems. Because more than 3000 active pharmaceutical ingredients (APIs) are in use, identifying high-priority pharmaceuticals is important for developing appropriate management options. Priority pharmaceuticals may vary by geographical region, because their occurrence levels can be influenced by demographic, societal, and regional characteristics. In the present study, the authors prioritized human pharmaceuticals of potential ecological risk in the Korean water environment, based on amount of use, biological activity, and regional hydrologic characteristics. For this purpose, the authors estimated the amounts of annual production of 695 human APIs in Korea. Then derived predicted environmental concentrations, using 2 approaches, to develop an initial candidate list of target pharmaceuticals. Major antineoplastic drugs and hormones were added in the initial candidate list regardless of their production amount because of their high biological activity potential. The predicted no effect concentrations were derived for those pharmaceuticals based on ecotoxicity information available in the literature or by model prediction. Priority lists of human pharmaceuticals were developed based on ecological risks and availability of relevant information. Those priority APIs identified include acetaminophen, clarithromycin, ciprofloxacin, ofloxacin, metformin, and norethisterone. Many of these pharmaceuticals have been neither adequately monitored nor assessed for risks in Korea. Further efforts are needed to improve these lists and to develop management decisions for these compounds in Korean water. © 2015 SETAC.

Risk analysis of heat recovery steam generator with semi quantitative risk based inspection API 581

NASA Astrophysics Data System (ADS)

Prayogo, Galang Sandy; Haryadi, Gunawan Dwi; Ismail, Rifky; Kim, Seon Jin

2016-04-01

Corrosion is a major problem that most often occurs in the power plant. Heat recovery steam generator (HRSG) is an equipment that has a high risk to the power plant. The impact of corrosion damage causing HRSG power plant stops operating. Furthermore, it could be threaten the safety of employees. The Risk Based Inspection (RBI) guidelines by the American Petroleum Institute (API) 58 has been used to risk analysis in the HRSG 1. By using this methodology, the risk that caused by unexpected failure as a function of the probability and consequence of failure can be estimated. This paper presented a case study relating to the risk analysis in the HRSG, starting with a summary of the basic principles and procedures of risk assessment and applying corrosion RBI for process industries. The risk level of each HRSG equipment were analyzed: HP superheater has a medium high risk (4C), HP evaporator has a medium-high risk (4C), and the HP economizer has a medium risk (3C). The results of the risk assessment using semi-quantitative method of standard API 581 based on the existing equipment at medium risk. In the fact, there is no critical problem in the equipment components. Damage mechanisms were prominent throughout the equipment is thinning mechanism. The evaluation of the risk approach was done with the aim of reducing risk by optimizing the risk assessment activities.

49 CFR 195.440 - Public awareness.

Code of Federal Regulations, 2014 CFR

2014-10-01

... Petroleum Institute's (API) Recommended Practice (RP) 1162 (incorporated by reference, see § 195.3). (b) The operator's program must follow the general program recommendations of API RP 1162 and assess the unique... general program recommendations, including baseline and supplemental requirements of API RP 1162, unless...

49 CFR 195.440 - Public awareness.

Code of Federal Regulations, 2013 CFR

2013-10-01

... Petroleum Institute's (API) Recommended Practice (RP) 1162 (incorporated by reference, see § 195.3). (b) The operator's program must follow the general program recommendations of API RP 1162 and assess the unique... general program recommendations, including baseline and supplemental requirements of API RP 1162, unless...

49 CFR 195.440 - Public awareness.

Code of Federal Regulations, 2012 CFR

2012-10-01

... Petroleum Institute's (API) Recommended Practice (RP) 1162 (incorporated by reference, see § 195.3). (b) The operator's program must follow the general program recommendations of API RP 1162 and assess the unique... general program recommendations, including baseline and supplemental requirements of API RP 1162, unless...

Prioritization of pharmaceuticals for potential environmental hazard through leveraging a large-scale mammalian pharmacological dataset.

PubMed

Berninger, Jason P; LaLone, Carlie A; Villeneuve, Daniel L; Ankley, Gerald T

2016-04-01

The potential for pharmaceuticals in the environment to cause adverse ecological effects is of increasing concern. Given the thousands of active pharmaceutical ingredients (APIs) that can enter the aquatic environment through human and/or animal (e.g., livestock) waste, a current challenge in aquatic toxicology is identifying those that pose the greatest risk. Because empirical toxicity information for aquatic species is generally lacking for pharmaceuticals, an important data source for prioritization is that generated during the mammalian drug development process. Applying concepts of species read-across, mammalian pharmacokinetic data were used to systematically prioritize APIs by estimating their potential to cause adverse biological consequences to aquatic organisms, using fish as an example. Mammalian absorption, distribution, metabolism, and excretion (ADME) data (e.g., peak plasma concentration, apparent volume of distribution, clearance rate, and half-life) were collected and curated, creating the Mammalian Pharmacokinetic Prioritization For Aquatic Species Targeting (MaPPFAST) database representing 1070 APIs. From these data, a probabilistic model and scoring system were developed and evaluated. Individual APIs and therapeutic classes were ranked based on clearly defined read-across assumptions for translating mammalian-derived ADME parameters to estimate potential hazard in fish (i.e., greatest predicted hazard associated with lowest mammalian peak plasma concentrations, total clearance and highest volume of distribution, half-life). It is anticipated that the MaPPFAST database and the associated API prioritization approach will help guide research and/or inform ecological risk assessment. Published 2015 Wiley Periodicals Inc. on behalf of SETAC. This article is a US Government work and, as such, is in the public domain in the United States of America.

Facies identification based on conventional core-log integration: Middle Ordovician St. Peter sandstone, Michigan basin

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

Wieczorek, L.M.; Barnes, D.A.

1989-08-01

Lithofacies comprising the massive sand in the Michigan basin are very similar to the lithofacies of the St. Peter Sandstone in parts of the adjacent Midwestern basin and arches region. Lithostratigraphic and biostratigraphic correlations justify application of the name St. Peter Sandstone to the gas-productive massive sand in the Michigan basin. Four lithofacies have been determined by core-log integration. The two lowermost lithofacies (1 and 2) were deposited in marginal-marine peritidal shoreface to sand-flat environments. Lithofacies 1A comprises cross-bedded, quartz-cemented quartzarenites. Lithofacies 1B comprises dolomitic, cross-bedded, subfeldspathic arenites. Lithofacies 1A is recognized in logs by low gamma-ray response (less thanmore » 20-25 API units) and photoelectric effect (Pe) of 1.8. Lithofacies 1B log characteristics include low gamma ray response (15-30 API units) and Pe of 2-2.5. Lithofacies 2 log signatures include moderate to high gamma-ray (30-120 API units) and Pe values that range from 2.5-3.5. The uppermost two lithofacies (3 and 4) were deposited in storm-dominated lower shoreface, to offshore, to distal marine shelf environments. Lithofacies 3 consists of burrowed, massive, wavy to planar stratified quartzarenites to subfeldspathic arenites. Log signature is generally low gamma-ray response (15-30 API units) and Pe that ranges from 1.8 to 2.5. Lithofacies 4 consists of massive, burrowed and bioturbated, dominantly authigenic clay and dolomite-cemented subfeldspathic arenite. Lithofacies 4 log response is moderate to high gamma-ray response (30-105 API units) and Pe ranging from 2.25 to 3.5.« less

Vaccinating Asian Pacific Islander children against hepatitis B: ethnic-specific influences and barriers.

PubMed

Pulido, M J; Alvarado, E A; Berger, W; Nelson, A; Todoroff, C

2001-01-01

Hepatitis B virus (HBV) is a known cause of liver cancer, especially among Asian and Pacific Islanders (API). Despite national recommendations and school entry requirements for vaccination, many children are not fully vaccinated with the Hepatitis B vaccine (Hep B) before entering school. The purpose of this study was to measure ethnic group-specific hepatitis B vaccination rates among school-aged API children after implementation of universal recommendations and school laws, and quantify ethnic-specific risk factors associated with late and incomplete vaccinations. A multilingual questionnaire was distributed to parents of second and fourth graders in nine Los Angeles County (LAC) elementary schools with high proportions of API students. Data on Hepatitis B vaccination dates, source of health care and health information, cultural factors, and general knowledge and attitudes about HBV and vaccination were collected and analyzed. Overall, 1,696 (77%) of 2,183 questionnaires were returned. Of these, 1,024 were from API children. The API second graders in this survey had a 72% coverage rate, ranging from 46% to 94% among the individual ethnic groups. Fifty-one percent of API fourth graders had three doses of Hep B vaccine, ranging from 38% to 69% among the individual ethnic groups. Factors influencing coverage levels among API fourth graders were speaking limited English at home, living in the United States less than five years, and not having discussed hepatitis B vaccination with a health care provider. Factors influencing low immunization levels differed among the API ethnic groups. Analysis and intervention on a non-aggregate level are necessary for designing both effective and cultural-specific outreach programs for diverse API communities such as LAC's.

Improved properties of fine active pharmaceutical ingredient powder blends and tablets at high drug loading via dry particle coating.

PubMed

Kunnath, Kuriakose; Huang, Zhonghui; Chen, Liang; Zheng, Kai; Davé, Rajesh

2018-05-30

It has been shown that dry coating cohesive active pharmaceutical ingredients (APIs) with nano-silica can improve packing and flow of their blends, facilitating high speed direct compression tableting. This paper examines the broader scope and generality of previous work by examining three fine APIs; micronized Acetaminophen (mAPAP), coarse Acetaminophen (cAPAP) and micronized Ibuprofen (mIBU), and considers dry coating with both hydrophobic or hydrophilic nano-silica to examine the effect not only on packing density and flow of their blends, but also dissolution and tensile strength of their tablets. The impact of the excipient size on blend and tablet properties are also investigated, indicating blend flow is most improved when matching API particle size with excipient particle size. In all cases where the API is dry coated, the blend packing and flow improve, so as to suggest such high drug loaded blends could enable direct compression. Using dry coated API along with finer excipients in blends lead to improved hardness of the corresponding tablets. Interestingly, dissolution profiles show dry coated API tablets generally have faster dissolution rates, regardless of silica hydrophilicity, suggesting API powder deagglomeration via nano-silica coating plays a crucial role. The most significant conclusion is that, although there are differences in properties of blends that depend on the API, hydrophobic or hydrophilic nano-silica coating, as well as large or fine excipients, in all cases, dry coating of APIs significantly improves the possibility of using the specific blend at high drug loading in direct compression tableting. Copyright © 2018 Elsevier B.V. All rights reserved.

49 CFR 192.616 - Public awareness.

Code of Federal Regulations, 2012 CFR

2012-10-01

... follows the guidance provided in the American Petroleum Institute's (API) Recommended Practice (RP) 1162... recommendations of API RP 1162 and assess the unique attributes and characteristics of the operator's pipeline and... supplemental requirements of API RP 1162, unless the operator provides justification in its program or...

49 CFR 192.616 - Public awareness.

Code of Federal Regulations, 2014 CFR

2014-10-01

... follows the guidance provided in the American Petroleum Institute's (API) Recommended Practice (RP) 1162... recommendations of API RP 1162 and assess the unique attributes and characteristics of the operator's pipeline and... supplemental requirements of API RP 1162, unless the operator provides justification in its program or...

49 CFR 192.616 - Public awareness.

Code of Federal Regulations, 2013 CFR

2013-10-01

... follows the guidance provided in the American Petroleum Institute's (API) Recommended Practice (RP) 1162... recommendations of API RP 1162 and assess the unique attributes and characteristics of the operator's pipeline and... supplemental requirements of API RP 1162, unless the operator provides justification in its program or...

Building model analysis applications with the Joint Universal Parameter IdenTification and Evaluation of Reliability (JUPITER) API

USGS Publications Warehouse

Banta, E.R.; Hill, M.C.; Poeter, E.; Doherty, J.E.; Babendreier, J.

2008-01-01

The open-source, public domain JUPITER (Joint Universal Parameter IdenTification and Evaluation of Reliability) API (Application Programming Interface) provides conventions and Fortran-90 modules to develop applications (computer programs) for analyzing process models. The input and output conventions allow application users to access various applications and the analysis methods they embody with a minimum of time and effort. Process models simulate, for example, physical, chemical, and (or) biological systems of interest using phenomenological, theoretical, or heuristic approaches. The types of model analyses supported by the JUPITER API include, but are not limited to, sensitivity analysis, data needs assessment, calibration, uncertainty analysis, model discrimination, and optimization. The advantages provided by the JUPITER API for users and programmers allow for rapid programming and testing of new ideas. Application-specific coding can be in languages other than the Fortran-90 of the API. This article briefly describes the capabilities and utility of the JUPITER API, lists existing applications, and uses UCODE_2005 as an example.

IFEQ, app developed based on the J-SHIS system

NASA Astrophysics Data System (ADS)

Azuma, H.; Hao, K. X.; Fujiwara, H.

2015-12-01

Raise an awareness of earthquake disaster prevention is an important issue in Japan. To do that, we have developed an app IFEQ on smartphone based on the APIs provided by the J-SHIS that is an integrated system of Seismic Hazard Assessment. IFEQ can simulate a real situation of earthquake disaster you might experience at current spot. The hint of the IFEQ came from a question "What should I do IF a big EarthQuake hit now?" An earthquake risk situation is estimated by a location information that is acquired from GPS, the detail comprehensive information of a 250m mesh obtained through J-SHIS APIs by the geomorphological classification and a probability of intensity 6 lower (JMA) within 30 years. A user's photo was displayed with a risk situation surrounded by simply one touch. IFEQ helps oneself to overcome a gap between exist scenes and a horrible disaster by enhancing imagination. The results show people have more ideas to handle with the risk situation after using the App IFEQ. IFEQ App's features are summarized as below: 1. Visualizing an image photo with possible risks from a coming earthquake at present spot. 2. Displaying an exceedance probability within 30-years and a maximum seismic intensity within 10,000-years on present location. 3. User can obtain some advices of how to prepare for possible risks. 4. A risk with five ranks is given, especially for items of Building Collapse, Liquefaction and Landslide. IFEQ can be downloaded freely from http://www.j-shis.bosai.go.jp/app-ifearthquake J-SHIS APIs can be obtained from http://www.j-shis.bosai.go.jp/en/category/opencat/api

Identification of bacteria in pasteurized zucchini purées stored at different temperatures and comparison with those found in other pasteurized vegetable purées.

PubMed

Guinebretiere, M H; Berge, O; Normand, P; Morris, C; Carlin, F; Nguyen-The, C

2001-10-01

One hundred nineteen isolates from a commercial zucchini purée stored at 4, 10, and 20 to 25 degrees C were fingerprinted using repetitive sequence-based PCR (REP-PCR) and classified into 35 REP types. One representative isolate of each REP type was subsequently identified by API50CHB/20E profile and partial rrs gene sequence analysis. Nine REP types were misidentified by the API system. Strains were misidentified as being in the Bacillus circulans (group 2) API taxon or in taxa with a low number of positive API characters such as Brevibacillus brevis. A phylogenetic analysis pointed to one new species of Bacillus and three new species of Paenibacillus among the misidentified REP types. Bacterial components in zucchini purée were compared phenotypically with those obtained in previous work on broccoli, carrot, leek, potato, and split pea purées, based on simple matching coefficient and unweighted pair group method with averages cluster analysis. Out of 254 strains, 69 strains previously identified as B. circulans (group 2) or B. circulans/B. macerans/B. polymyxa were assigned to a new Paenibacillus taxon phylogenetically related to P. azotofixans. Storage conditions at 4 degrees C favored the development of "B. macroides/B. maroccanus" and Paenibacillus spp. in zucchini purées and Paenibacillus spp. in other purées. Storage conditions at 20 to 25 degrees C favored the development of B. subtilis group (B. licheniformis and B. subtilis) and B. cereus group strains. At 10 degrees C, Paenibacillus spp. were always present at high frequencies, whereas the occurrence of B. macroides/B. maroccanus (in zucchini purées), B. cereus, and B. pumilus varied with the experiment.

Identification of Bacteria in Pasteurized Zucchini Purées Stored at Different Temperatures and Comparison with Those Found in Other Pasteurized Vegetable Purées

PubMed Central

Guinebretiere, Marie-Hélène; Berge, Odile; Normand, Philippe; Morris, Cindy; Carlin, Frédéric; Nguyen-The, Christophe

2001-01-01

One hundred nineteen isolates from a commercial zucchini purée stored at 4, 10, and 20 to 25°C were fingerprinted using repetitive sequence-based PCR (REP-PCR) and classified into 35 REP types. One representative isolate of each REP type was subsequently identified by API50CHB/20E profile and partial rrs gene sequence analysis. Nine REP types were misidentified by the API system. Strains were misidentified as being in the Bacillus circulans (group 2) API taxon or in taxa with a low number of positive API characters such as Brevibacillus brevis. A phylogenetic analysis pointed to one new species of Bacillus and three new species of Paenibacillus among the misidentified REP types. Bacterial components in zucchini purée were compared phenotypically with those obtained in previous work on broccoli, carrot, leek, potato, and split pea purées, based on simple matching coefficient and unweighted pair group method with averages cluster analysis. Out of 254 strains, 69 strains previously identified as B. circulans (group 2) or B. circulans/B. macerans/B. polymyxa were assigned to a new Paenibacillus taxon phylogenetically related to P. azotofixans. Storage conditions at 4°C favored the development of “B. macroides/B. maroccanus” and Paenibacillus spp. in zucchini purées and Paenibacillus spp. in other purées. Storage conditions at 20 to 25°C favored the development of B. subtilis group (B. licheniformis and B. subtilis) and B. cereus group strains. At 10°C, Paenibacillus spp. were always present at high frequencies, whereas the occurrence of B. macroides/B. maroccanus (in zucchini purées), B. cereus, and B. pumilus varied with the experiment. PMID:11571151

A novel air pollution index based on the relative risk of daily mortality associated with short-term exposure to common air pollutants

NASA Astrophysics Data System (ADS)

Cairncross, Eugene K.; John, Juanette; Zunckel, Mark

Communication of the complex relationship between air pollutant exposure and ill health is essential to an air pollution information system. We propose a novel air pollution index (API) system based on the relative risk of the well-established increased daily mortality associated with short-term exposure to common air pollutants: particulate matter (PM 10, PM 2.5), sulphur dioxide, ozone, nitrogen dioxide and carbon monoxide. To construct our index system, the total incremental daily mortality risk of exposure to these pollutants was associated with an index value ranging from 0 to 10. The index scale is linear with respect to incremental risk. The index is open ended, although, for convenience, an index of 10 is assigned for exposures yielding indices ⩾10. To illustrate the application of this API system, a set of published relative risk factors are used to calculate sub-index values for each pollutant, in the range of air pollutant concentrations commonly experienced in urban areas. To account for the reality of ubiquitous simultaneous exposure to a mixture of the common air pollutants, the final API is the sum of the normalised values of the individual indices for PM 10, PM 2.5, sulphur dioxide, ozone, nitrogen dioxide and carbon monoxide. This establishes a self-consistent index system where a given index value corresponds to the same daily mortality risk associated with the combined exposure to the common air pollutants. To facilitate health-risk communication, index values are colour coded and associated with broad health-risk descriptors. The utility of the proposed API is illustrated by applying it to monitored ambient concentration data for the City of Cape Town, South Africa.

Comparative analysis of detection limits and specificity of molecular diagnostic markers for three pathogens (Microsporidia, Nosema spp.) in the key pollinators Apis mellifera and Bombus terrestris.

PubMed

Erler, Silvio; Lommatzsch, Stefanie; Lattorff, H Michael G

2012-04-01

Global pollinator decline has recently been discussed in the context of honey and bumble bee infections from various pathogens including viruses, bacteria, microsporidia and mites. The microsporidian pathogens Nosema apis, Nosema ceranae and Nosema bombi may in fact be major candidates contributing to this decline. Different molecular and non-molecular detection methods have been developed; however, a comparison, especially of the highly sensitive PCR based methods, is currently lacking. Here, we present the first comparative quantitative real-time PCR study of nine Nosema spp. primers within the framework of primer specificity and sensitivity. With the help of dilution series of defined numbers of spores, we reveal six primer pairs amplifying N. apis, six for N. bombi and four for N. ceranae. All appropriate primer pairs detected an amount of at least 10(4) spores, the majority of which were even as sensitive to detect such low amounts as 10(3) to ten spores. Species specificity of primers was observed for N. apis and N. bombi, but not for N. ceranae. Additionally, we did not find any significant correlation for the amplified fragments with PCR efficiency or the limit of detection. We discuss our findings on the background of false positive and negative results using quantitative real-time PCR. On the basis of these results, future research might be based on appropriate primer selection depending on the experimental needs. Primers may be selected on the basis of specificity or sensitivity. Pathogen species and load may be determined with higher precision enhancing all kinds of diagnostic studies.

Alcohol Control Policies and Alcohol Consumption by Youth: A Multi-National Study

PubMed Central

Paschall, Mallie J.; Grube, Joel W.; Kypri, Kypros

2009-01-01

Aims The study examined relationships between alcohol control policies and adolescent alcohol use in 26 countries. Design Cross-sectional analyses of alcohol policy ratings based on the Alcohol Policy Index (API), per capita consumption, and national adolescent survey data. Setting Data are from 26 countries. Participants Adolescents (15-17 years old) who participated in the 2003 ESPAD (European countries) or national secondary school surveys in Spain, Canada, Australia, New Zealand and the USA. Measurements Alcohol control policy ratings based on the API; prevalence of alcohol use, heavy drinking, and first drink by age 13 based on national secondary school surveys; per capita alcohol consumption for each country in 2003. Analysis Correlational and linear regression analyses were conducted to examine relationships between alcohol control policy ratings and past-30-day prevalence of adolescent alcohol use, heavy drinking, and having first drink by age 13. Per capita consumption of alcohol was included as a covariate in regression analyses. Findings More comprehensive API ratings and alcohol availability and advertising control ratings were inversely related to the past-30-day prevalence of alcohol use and prevalence rates for drinking 3-5 times and 6 or more times in the past 30 days. Alcohol advertising control was also inversely related to the prevalence of past-30-day heavy drinking and having first drink by age 13. Most of the relationships between API, alcohol availability and advertising control and drinking prevalence rates were attenuated and no longer statistically significant when controlling for per capita consumption in regression analyses, suggesting that alcohol use in the general population may confound or mediate observed relationships between alcohol control policies and youth alcohol consumption. Several of the inverse relationships remained statistically significant when controlling for per capita consumption. Conclusions More comprehensive and stringent alcohol control policies, particularly policies affecting alcohol availability and marketing, are associated with lower prevalence and frequency of adolescent alcohol consumption and age of first alcohol use. PMID:19832785

Modelface: an Application Programming Interface (API) for Homology Modeling Studies Using Modeller Software

PubMed Central

Sakhteman, Amirhossein; Zare, Bijan

2016-01-01

An interactive application, Modelface, was presented for Modeller software based on windows platform. The application is able to run all steps of homology modeling including pdb to fasta generation, running clustal, model building and loop refinement. Other modules of modeler including energy calculation, energy minimization and the ability to make single point mutations in the PDB structures are also implemented inside Modelface. The API is a simple batch based application with no memory occupation and is free of charge for academic use. The application is also able to repair missing atom types in the PDB structures making it suitable for many molecular modeling studies such as docking and molecular dynamic simulation. Some successful instances of modeling studies using Modelface are also reported. PMID:28243276

Required ozone doses for removing pharmaceuticals from wastewater effluents.

PubMed

Antoniou, Maria G; Hey, Gerly; Rodríguez Vega, Sergio; Spiliotopoulou, Aikaterini; Fick, Jerker; Tysklind, Mats; la Cour Jansen, Jes; Andersen, Henrik Rasmus

2013-07-01

The aim of the this study was to investigate the ozone dosage required to remove active pharmaceutical ingredients (APIs) from biologically treated wastewater of varying quality, originated from different raw wastewater and wastewater treatment processes. Secondary effluents from six Swedish wastewater treatment plants (WWTP) were spiked with 42 APIs (nominal concentration μg/L) and treated with different O₃ doses (0.5-12.0 mg/L ozone) in bench-scale experiments. In order to compare the sensitivity of APIs in each matrix, the specific dose of ozone required to achieve reduction by one decade of each investigated API (DDO₃) was determined for each effluent by fitting a first order equation to the remaining concentration of API at each applied ozone dose. Ozone dose requirements were found to vary significantly between effluents depending on their matrix characteristics. The specific ozone dose was then normalized to the dissolved organic carbon (DOC) of each effluent. The DDO₃/DOC ratios were comparable for each API between the effluents. 15 of the 42 investigated APIs could be classified as easily degradable (DDO₃/DOC ≤ 0.7), while 19 were moderately degradable (0.7 < DDO₃/DOC ≤ 1.4), and 8 were recalcitrant towards O₃-treatment (DDO₃/DOC >1.4). Furthermore, we predict that a reasonable estimate of the ozone dose required to remove any of the investigated APIs may be attained by multiplying the experimental average DDO₃/DOC obtained with the actual DOC of any effluent. Copyright © 2013 Elsevier B.V. All rights reserved.

Perinatal outcomes for Asian, Native Hawaiian, and other Pacific Islander mothers of single and multiple race/ethnicity: California and Hawaii, 2003-2005.

PubMed

Schempf, Ashley H; Mendola, Pauline; Hamilton, Brady E; Hayes, Donald K; Makuc, Diane M

2010-05-01

We examined characteristics and birth outcomes of Asian/Pacific Islander (API) mothers to determine whether differences in outcomes existed between mothers of single race/ethnicity and multiple race/ethnicity. We used data from California and Hawaii birth certificates from 2003 through 2005 to describe variation in birth outcomes for API subgroups by self-reported maternal race/ethnicity (single versus multiple race or API subgroup), and we also compared these outcomes to those of non-Hispanic White women. Low birthweight (LBW) and preterm birth (PTB) varied more among API subgroups than between mothers of single versus multiple race/ethnicity. After adjustment for sociodemographic and behavioral risk factors, API mothers of multiple race/ethnicity had outcomes similar to mothers of single race/ethnicity, with exceptions for multiple-race/ethnicity Chinese (higher PTB), Filipino (lower LBW and PTB), and Thai (higher LBW) subgroups. Compared with single-race non-Hispanic Whites, adverse outcomes were elevated for most API subgroups: only single-race/ethnicity Korean mothers had lower rates of both LBW (3.4%) and PTB (5.6%); single-race/ethnicity Cambodian, Laotian, and Marshallese mothers had the highest rates of both LBW (8.8%, 9.2%, and 8.4%, respectively) and PTB (14.0%, 13.7%, and 18.8%, respectively). Strategies to improve birth outcomes for API mothers should consider variations in risk by API subgroup and multiple race/ethnicity.

Pim-2 activates API-5 to inhibit the apoptosis of hepatocellular carcinoma cells through NF-kappaB pathway.

PubMed

Ren, Ke; Zhang, Wei; Shi, Yujun; Gong, Jianping

2010-06-01

Pim-2 is proved to be relevant to the tumorigenesis of hepatocellular carcinoma (HCC), but the mechanism is unclear. We studied the relationship among Pim-2, NF-kappaB and API-5. In our experiment, expression level of the three factors and phosphorylation level of API-5, as well as NF-kappaB activity, were detected in HCC tissues and the nontumorous controls. Then Pim-2 gene was transfected into nontumorous liver cells L02, and Pim-2 SiRNA was transfected into hepatoblastoma cell line HepG2. Parthenolide was added as NF-kappaB inhibitor. The same detections as above were repeated in the cells, along with the apoptosis analysis. We found the levels of Pim-2, NF-kappaB and API-5, as well as NF-kappaB activity, were significantly higher in HCC tissues. Pim-2 level was increased in L02 cells after the transfection of Pim-2 gene, but decreased in HepG2 cells after the transfection of Pim-2 SiRNA. The levels of NF-kappaB and API-5, as well as NF-kappaB activity and API-5 phosphorylation level, were in accordance with Pim-2 level, but could be reversed by Parthenolide. Cell apoptosis rates were negatively correlated with API-5 phosphorylation level. Therefore, we infer that Pim-2 could activate API-5 to inhibit the apoptosis of liver cells, and NF-kappaB is the key regulator.

Updates to the NASA Space Telecommunications Radio System (STRS) Architecture

NASA Technical Reports Server (NTRS)

Kacpura, Thomas J.; Handler, Louis M.; Briones, Janette; Hall, Charles S.

2008-01-01

This paper describes an update of the Space Telecommunications Radio System (STRS) open architecture for NASA space based radios. The STRS architecture has been defined as a framework for the design, development, operation and upgrade of space based software defined radios, where processing resources are constrained. The architecture has been updated based upon reviews by NASA missions, radio providers, and component vendors. The STRS Standard prescribes the architectural relationship between the software elements used in software execution and defines the Application Programmer Interface (API) between the operating environment and the waveform application. Modeling tools have been adopted to present the architecture. The paper will present a description of the updated API, configuration files, and constraints. Minimum compliance is discussed for early implementations. The paper then closes with a summary of the changes made and discussion of the relevant alignment with the Object Management Group (OMG) SWRadio specification, and enhancements to the specialized signal processing abstraction.

Mass data graphics requirements for symbol generators: example 2D airport navagation and 3D terrain function

NASA Astrophysics Data System (ADS)

Schiefele, Jens; Bader, Joachim; Kastner, S.; Wiesemann, Thorsten; von Viebahn, Harro

2002-07-01

Next generation of cockpit display systems will display mass data. Mass data includes terrain, obstacle, and airport databases. Display formats will be two and eventually 3D. A prerequisite for the introduction of these new functions is the availability of certified graphics hardware. The paper describes functionality and required features of an aviation certified 2D/3D graphics board. This graphics board should be based on low-level and hi-level API calls. These graphic calls should be very similar to OpenGL. All software and the API must be aviation certified. As an example application, a 2D airport navigation function and a 3D terrain visualization is presented. The airport navigation format is based on highly precise airport database following EUROCAE ED-99/RTCA DO-272 specifications. Terrain resolution is based on EUROCAE ED-98/RTCA DO-276 requirements.

Test Operations Procedure (TOP) 02-2-603A Vehicle Fuel Consumption

DTIC Science & Technology

2012-05-10

API) Hydrometer . The API Hydrometer is used for accurate determination of the density, relative density (specific gravity), or API gravity of... Hydrometer Method. 5. TOP 02-2-505, Inspection and Preliminary Operation of Vehicles, 4 February 1987. 6. TOP 02-1-003, Hybrid Electric

The position of the anal dimple in newborns and infants with anorectal malformations and its correlation with the normal anal position.

PubMed

Patel, Jigar N; Kumar, Amit; Yadav, Partap Singh; Chadha, Rajiv; Datta, Vikram; Roy Choudhury, Subhasis

2017-11-16

The anal position index (API) defines the normal anal position as the ratio of fourchette-anal distance to fourchette-coccyx distance for females and the scrotum-anal distance to scrotum-coccyx distance for males. In this study, measurement of the API in newborns and infants with anorectal malformations (ARM), using the center of the midline anal dimple (AD) to represent the center of the proposed neoanus, was performed to assess whether or not the AD was located in a significantly abnormal position as correlated with the normal anal position. The cases comprised 65 consecutive newborn and infants with ARM, divided into 2 age-based groups (Group A: 1st day to 1month; Group B: 1-12months), without sacral or significant perineal abnormalities. Controls included an equal number of age and gender matched patients admitted for other conditions. The characteristics of the AD ('well developed' or 'moderately developed') as well as those of the midline perineal raphé in males and the perineal groove in females were also recorded. Combining both age groups, the mean API±SD was 0.41±0.012 in male cases and 0.53±0.07 in male controls (p value 0.003). The corresponding values for female cases and controls were 0.31±0.09 and 0.36±0.07 respectively (p = 0.040). In male newborns, the API in cases was significantly lower than the API in controls (p<0.001). Combining both males and female newborns, the differences between the API in cases and controls was also statistically significant (p<0.001). In older boys as well as in girls from both age groups, apart from cases of persistent cloaca, the API was lower in cases than in controls, especially in boys, although the difference was not statistically significant. On comparing the API in individual male ARM with that in male controls, cases of rectobulbar urethral fistula (RBUF) and rectovesical fistula had a statistically significant lower API (p<0.001). In the 4 cases of persistent cloaca, the mean API (0.40±0.1) was higher than the mean API in female controls and the AD was well developed with a well-delineated, narrow perineal groove. The majority (53/65; 81.53%) of patients had a 'well developed' AD. Twelve patients (18.47%) had a 'moderately developed' AD including 10 females and 2 males. There were 15 patients with a depressed AD (anal fossette); of these 12 (80%) were females. All boys had a well delineated perineal raphé in contrast to 10 girls (29.4% of total female ARM) who had a poorly delineated midline perineal groove. During definitive surgery for ARM, if the AD is taken as the site of the proposed neoanus, the neoanal position is likely to be anterior to the normal anal position in both males and females and especially so in males. Overall, girls with ARM appear to be more likely to have a relatively poorly developed and/ or depressed AD and a poorly delineated perineal groove. Clinical Research. Level III. Copyright © 2017 Elsevier Inc. All rights reserved.

Different bees, different needs: how nest-site requirements have shaped the decision-making processes in homeless honeybees (Apis spp.).

PubMed

Beekman, Madeleine; Oldroyd, Benjamin P

2018-05-19

During reproductive swarming, a honeybee swarm needs to decide on a new nest site and then move to the chosen site collectively. Most studies of swarming and nest-site selection are based on one species, Apis mellifera Natural colonies of A. mellifera live in tree cavities. The quality of the cavity is critical to the survival of a swarm. Other honeybee species nest in the open, and have less strict nest-site requirements, such as the open-nesting dwarf honeybee Apis florea Apis florea builds a nest comprised of a single comb suspended from a twig. For a cavity-nesting species, there is only a limited number of potential nest sites that can be located by a swarm, because suitable sites are scarce. By contrast, for an open-nesting species, there is an abundance of equally suitable twigs. While the decision-making process of cavity-nesting bees is geared towards selecting the best site possible, open-nesting species need to coordinate collective movement towards areas with potential nest sites. Here, we argue that the nest-site selection processes of A. florea and A. mellifera have been shaped by each species' specific nest-site requirements. Both species use the same behavioural algorithm, tuned to allow each species to solve their species-specific problem.This article is part of the theme issue 'Collective movement ecology'. © 2018 The Author(s).

Formulation and process factors influencing product quality and in vitro performance of ophthalmic ointments.

PubMed

Xu, Xiaoming; Al-Ghabeish, Manar; Rahman, Ziyaur; Krishnaiah, Yellela S R; Yerlikaya, Firat; Yang, Yang; Manda, Prashanth; Hunt, Robert L; Khan, Mansoor A

2015-09-30

Owing to its unique anatomical and physiological functions, ocular surface presents special challenges for both design and performance evaluation of the ophthalmic ointment drug products formulated with a variety of bases. The current investigation was carried out to understand and identify the appropriate in vitro methods suitable for quality and performance evaluation of ophthalmic ointment, and to study the effect of formulation and process variables on its critical quality attributes (CQA). The evaluated critical formulation variables include API initial size, drug percentage, and mineral oil percentage while the critical process parameters include mixing rate, temperature, time and cooling rate. The investigated quality and performance attributes include drug assay, content uniformity, API particle size in ointment, rheological characteristics, in vitro drug release and in vitro transcorneal drug permeation. Using design of experiments (DoE) as well as a novel principle component analysis approach, five of the quality and performance attributes (API particle size, storage modulus of ointment, high shear viscosity of ointment, in vitro drug release constant and in vitro transcorneal drug permeation rate constant) were found to be highly influenced by the formulation, in particular the strength of API, and to a lesser degree by processing variables. Correlating the ocular physiology with the physicochemical characteristics of acyclovir ophthalmic ointment suggested that in vitro quality metrics could be a valuable predictor of its in vivo performance. Published by Elsevier B.V.

Experience API: Flexible, Decentralized and Activity-Centric Data Collection

ERIC Educational Resources Information Center

Kevan, Jonathan M.; Ryan, Paul R.

2016-01-01

This emerging technology report describes the Experience API (xAPI), a new e-learning specification designed to support the learning community in standardizing and collecting both formal and informal distributed learning activities. Informed by Activity Theory, a framework aligned with constructivism, data is collected in the form of activity…

wbstats

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

Piburn, Jesse

2016-04-22

Availability of accessing the World Bank Data API through the R language was limited to one existing package, which is limited in its ability. The software provides access to all of the features in World Bank API in one software package for the R language and provides functions for searching and downloading data from the World Bank API.

30 CFR 250.114 - How must I install and operate electrical equipment?

Code of Federal Regulations, 2010 CFR

2010-07-01

.... (a) You must classify all areas according to API RP 500, Recommended Practice for Classification of... Division 2, or API RP 505, Recommended Practice for Classification of Locations for Electrical... and hazards of electrical equipment. (c) You must install all electrical systems according to API RP...

49 CFR 195.428 - Overpressure safety devices and overfill protection systems.

Code of Federal Regulations, 2011 CFR

2011-10-01

... API Standard 2510 after October 2, 2000, must have an overfill protection system installed according to section 5.1.2 of API Standard 2510. Other aboveground breakout tanks with 600 gallons (2271 liters... have an overfill protection system installed according to API Recommended Practice 2350. However...

30 CFR 250.1203 - Gas measurement.

Code of Federal Regulations, 2013 CFR

2013-07-01

... follow the recommendations in API MPMS or RP and AGA as incorporated by reference in 30 CFR 250.198, including the following additional editions: (i) API RP 86 (incorporated by reference as specified in § 250.... If an electronic data recorder is used, you must follow the recommendations in API MPMS. (5) Take...

49 CFR 195.428 - Overpressure safety devices and overfill protection systems.

Code of Federal Regulations, 2014 CFR

2014-10-01

... API Standard 2510 after October 2, 2000, must have an overfill protection system installed according to section 5.1.2 of API Standard 2510. Other aboveground breakout tanks with 600 gallons (2271 liters... have an overfill protection system installed according to API Recommended Practice 2350. However...

49 CFR 195.428 - Overpressure safety devices and overfill protection systems.

Code of Federal Regulations, 2013 CFR

2013-10-01

... API Standard 2510 after October 2, 2000, must have an overfill protection system installed according to section 5.1.2 of API Standard 2510. Other aboveground breakout tanks with 600 gallons (2271 liters... have an overfill protection system installed according to API Recommended Practice 2350. However...

30 CFR 250.1203 - Gas measurement.

Code of Federal Regulations, 2014 CFR

2014-07-01

... follow the recommendations in API MPMS or RP and AGA as incorporated by reference in 30 CFR 250.198, including the following additional editions: (i) API RP 86 (incorporated by reference as specified in § 250.... If an electronic data recorder is used, you must follow the recommendations in API MPMS. (5) Take...

30 CFR 250.1203 - Gas measurement.

Code of Federal Regulations, 2012 CFR

2012-07-01

... follow the recommendations in API MPMS or RP and AGA as incorporated by reference in 30 CFR 250.198, including the following additional editions: (i) API RP 86 (incorporated by reference as specified in § 250.... If an electronic data recorder is used, you must follow the recommendations in API MPMS. (5) Take...

49 CFR 195.428 - Overpressure safety devices and overfill protection systems.

Code of Federal Regulations, 2012 CFR

2012-10-01

... API Standard 2510 after October 2, 2000, must have an overfill protection system installed according to section 5.1.2 of API Standard 2510. Other aboveground breakout tanks with 600 gallons (2271 liters... have an overfill protection system installed according to API Recommended Practice 2350. However...

AN OVERVIEW OF THE UNCERTAINTY ANALYSIS, SENSITIVITY ANALYSIS, AND PARAMETER ESTIMATION (UA/SA/PE) API AND HOW TO IMPLEMENT IT

EPA Science Inventory

The Application Programming Interface (API) for Uncertainty Analysis, Sensitivity Analysis, and
Parameter Estimation (UA/SA/PE API) (also known as Calibration, Optimization and Sensitivity and Uncertainty (CUSO)) was developed in a joint effort between several members of both ...

77 FR 70142 - Initialed Draft Revision to the Agreement Suspending the Antidumping Investigation on Certain Hot...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-23

...; API 5L Grades A & B....... Two--HSLA & HSLA-F Quality Grades: A572, A1011-HSLAS; A1018-HSLAS, A1011-HSLAS- $661.92 F; A1018-HSLAS-F; API 5L Gr. X42, X46, X52, X56, X60; API 5CT Grades J55 and K55 Three--High Grade Coils and Sheets for Pipes and Casings API 5L Gr. X65, X70, and X80 $770.24 Section III.E is...

The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles

PubMed Central

Buske, Orion J.; Schiettecatte, François; Hutton, Benjamin; Dumitriu, Sergiu; Misyura, Andriy; Huang, Lijia; Hartley, Taila; Girdea, Marta; Sobreira, Nara; Mungall, Chris; Brudno, Michael

2016-01-01

Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously-identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis. PMID:26255989

Presence of active pharmaceutical ingredients in the continuum of surface and ground water used in drinking water production.

PubMed

Ahkola, Heidi; Tuominen, Sirkku; Karlsson, Sanja; Perkola, Noora; Huttula, Timo; Saraperä, Sami; Artimo, Aki; Korpiharju, Taina; Äystö, Lauri; Fjäder, Päivi; Assmuth, Timo; Rosendahl, Kirsi; Nysten, Taina

2017-12-01

Anthropogenic chemicals in surface water and groundwater cause concern especially when the water is used in drinking water production. Due to their continuous release or spill-over at waste water treatment plants, active pharmaceutical ingredients (APIs) are constantly present in aquatic environment and despite their low concentrations, APIs can still cause effects on the organisms. In the present study, Chemcatcher passive sampling was applied in surface water, surface water intake site, and groundwater observation wells to estimate whether the selected APIs are able to end up in drinking water supply through an artificial groundwater recharge system. The API concentrations measured in conventional wastewater, surface water, and groundwater grab samples were assessed with the results obtained with passive samplers. Out of the 25 APIs studied with passive sampling, four were observed in groundwater and 21 in surface water. This suggests that many anthropogenic APIs released to waste water proceed downstream and can be detectable in groundwater recharge. Chemcatcher passive samplers have previously been used in monitoring several harmful chemicals in surface and wastewaters, but the path of chemicals to groundwater has not been studied. This study provides novel information on the suitability of the Chemcatcher passive samplers for detecting APIs in groundwater wells.

Dry coating of micronized API powders for improved dissolution of directly compacted tablets with high drug loading.

PubMed

Han, Xi; Ghoroi, Chinmay; Davé, Rajesh

2013-02-14

Motivated by our recent study showing improved flow and dissolution rate of the active pharmaceutical ingredient (API) powders (20 μm) produced via simultaneous micronization and surface modification through continuous fluid energy milling (FEM) process, the performance of blends and direct compacted tablets with high drug loading is examined. Performance of 50 μm API powders dry coated without micronization is also considered for comparison. Blends of micronized, non-micronized, dry coated or uncoated API powders at 30, 60 and 70% drug loading, are examined. The results show that the blends containing dry coated API powders, even micronized ones, have excellent flowability and high bulk density compared to the blends containing uncoated API, which are required for direct compaction. As the drug loading increases, the difference between dry coated and uncoated blends is more pronounced, as seen in the proposed bulk density-FFC phase map. Dry coating led to improved tablet compactibility profiles, corresponding with the improvements in blend compressibility. The most significant advantage is in tablet dissolution where for all drug loadings, the t(80) for the tablets with dry coated APIs was well under 5 min, indicating that this approach can produce nearly instant release direct compacted tablets at high drug loadings. Copyright © 2012 Elsevier B.V. All rights reserved.

Alpha 1-protease inhibitor moderates human neutrophil elastase-induced emphysema and secretory cell metaplasia in hamsters.

PubMed

Stone, P J; Lucey, E C; Virca, G D; Christensen, T G; Breuer, R; Snider, G L

1990-06-01

A study was undertaken to determine whether emphysema and airway secretory cell metaplasia, induced in hamsters by intratracheal treatment with human neutrophil elastase (HNE), could be moderated by pretreatment with human alpha 1-protease inhibitor (API). API (4.9 mg) was given intratracheally to hamsters 1 h before 0.3 mg HNE. Eight weeks later, lung volumes and pressure-volume relationships were measured in the anaesthetized animals. Mean linear intercepts and secretory cell indices were measured in lung sections. API given 1 h before HNE moderated the development of bronchial secretory cell metaplasia. The severity of emphysema was reduced by 75%. Clearance studies indicated that 80% of the functional activity of instilled API could be lavaged from the lungs after 1 h, indicating a 4 h half-life in the lavageable compartment of the lungs. We calculate that for 50% protection from emphysema the molar ratio of lavageable API to HNE at the time of HNE instillation was 4.8 as compared with 0.78 for 50% inhibition of elastolytic activity in vitro, indicating that API is only 16% as efficient in vivo as compared with its in vitro HNE inhibitory effectiveness. Nevertheless, we conclude that human API given intratracheally is efficacious against HNE-induced emphysema and secretory cell metaplasia.

Higher prevalence and levels of Nosema ceranae than Nosema apis infections in Canadian honey bee colonies.

PubMed

Emsen, Berna; Guzman-Novoa, Ernesto; Hamiduzzaman, Mollah Md; Eccles, Les; Lacey, Brian; Ruiz-Pérez, Rosario A; Nasr, Medhat

2016-01-01

This study was conducted to determine the prevalence and infection levels of the microsporidia fungi Nosema apis and/or Nosema ceranae in honey bee colonies of two Canadian provinces. Three surveys were conducted in the springs of 2008, 2010 and 2012 and PCR identification of Nosema species were performed in samples from 169 and 181 Ontario colonies and from 76 Alberta colonies that tested positive to Nosema spp. Infection levels of positive colonies were determined by microscopy and analyzed by Nosema spp. Results showed that N. ceranae was the dominant species in all three surveys (prevalence range of 41-91 vs. 4-34 % for N. apis), whereas mixed infections were less frequent than single infections (5-25 %). Infection levels of colonies parasitized by N. ceranae were three to five times higher than those of colonies parasitized by N. apis in the three surveys whereas mixed infections showed the highest spore counts. This is the first field study demonstrating significantly higher infection levels in colonies parasitized with either N. ceranae only or with both, N. ceranae and N. apis, than in colonies parasitized with N. apis only. Taken together, these results suggest that N. ceranae may be more virulent and better adapted than N. apis in cold climates such as Canadian environments.

The Matchmaker Exchange API: automating patient matching through the exchange of structured phenotypic and genotypic profiles.

PubMed

Buske, Orion J; Schiettecatte, François; Hutton, Benjamin; Dumitriu, Sergiu; Misyura, Andriy; Huang, Lijia; Hartley, Taila; Girdea, Marta; Sobreira, Nara; Mungall, Chris; Brudno, Michael

2015-10-01

Despite the increasing prevalence of clinical sequencing, the difficulty of identifying additional affected families is a key obstacle to solving many rare diseases. There may only be a handful of similar patients worldwide, and their data may be stored in diverse clinical and research databases. Computational methods are necessary to enable finding similar patients across the growing number of patient repositories and registries. We present the Matchmaker Exchange Application Programming Interface (MME API), a protocol and data format for exchanging phenotype and genotype profiles to enable matchmaking among patient databases, facilitate the identification of additional cohorts, and increase the rate with which rare diseases can be researched and diagnosed. We designed the API to be straightforward and flexible in order to simplify its adoption on a large number of data types and workflows. We also provide a public test data set, curated from the literature, to facilitate implementation of the API and development of new matching algorithms. The initial version of the API has been successfully implemented by three members of the Matchmaker Exchange and was immediately able to reproduce previously identified matches and generate several new leads currently being validated. The API is available at https://github.com/ga4gh/mme-apis. © 2015 WILEY PERIODICALS, INC.

Degradation of Artemisinin-Based Combination Therapies Under Tropical Conditions.

PubMed

Hall, Zoe; Allan, Elizabeth Louise; van Schalkwyk, Donelly Andrew; van Wyk, Albert; Kaur, Harparkash

2016-05-04

Poor quality antimalarials, including falsified, substandard, and degraded drugs, are a serious health concern in malaria-endemic countries. Guidelines are lacking on how to distinguish between substandard and degraded drugs. "Forced degradation" in an oven was carried out on three common artemisinin-based combination therapy (ACT) brands to detect products of degradation using liquid chromatography mass spectrometry and help facilitate classification of degraded drugs. "Natural aging" of 2,880 tablets each of ACTs artemether/lumefantrine and artesunate/amodiaquine was undertaken to evaluate their long-term stability in tropical climates. Samples were aged in the presence and absence of light on-site in Ghana and in a stability chamber (London), removed at regular intervals, and analyzed to determine loss of the active pharmaceutical ingredients (APIs) over time and detect products of degradation. Loss of APIs in naturally aged tablets (both in Ghana and the pharmaceutical stability chamber) was 0-7% over 3 years (∼12 months beyond expiry) with low levels of degradation products detected. Using this developed methodology, it was found that a quarter of ACTs purchased in Enugu, Nigeria (concurrent study), that would have been classified as substandard, were in fact degraded. Presence of degradation products together with evidence of insufficient APIs can be used to classify drugs as degraded. © The American Society of Tropical Medicine and Hygiene.

Synthesis, characterization and dissolution of three pharmaceutical cocrystals based on deferiprone

NASA Astrophysics Data System (ADS)

Zhang, Xiaoming; Tian, Yuyang; Jia, Jiangtao; Zhang, Tingting; Zhu, Guangshan

2016-03-01

In this paper we present three new cocrystals based on deferiprone which is the first oral medicine as iron chelator. Solitary deferiprone possesses some known problems due to its good solubility and frequent dosing side effects. For these three novel co crystals, deferiprone is the active pharmaceutical ingredient (API), p-hydroxybenzoic acid (1, C7H9NO2·C7H6O3), 2, 5-dihydroxybenzoic acid (2, C7H9NO2·C7H6O4) and maleic acid (3, C7H9NO2·C4H4O4) are used as cocrystal formers (CCFs), respectively. Their structures were characterized by single crystal X-ray diffraction, powder X-ray diffraction (PXRD) analysis, thermogravimetric analyses (TGA), differential thermal analysis (DTA), elemental analysis (EA) and infrared spectral analysis (IR). Single crystal X-ray diffraction demonstrates that all three cocrystals (1-3) possess strong hydrogen-bondings assembled through hydroxyl of API and carboxylic acids of CCFs. The PXRD results indicate their high purity of as-synthesized samples. TGA, DTA, EA, IR and dissolution study of API and cocrystals were also measured and discussed, respectively. The results suggest that the cocrystals exhibit low dissolution rates comparing with solitary deferiprone, which is very advantageous for the oral medicine with frequent dosing side effects.

Maintaining the momentum of Open Search in Earth Science Data discovery

NASA Astrophysics Data System (ADS)

Newman, D. J.; Lynnes, C.

2013-12-01

Federated Search for Earth Observation data has been a hallmark of EOSDIS (Earth Observing System Data and Information System) for two decades. Originally, the EOSDIS Version 0 system provided both data-collection-level and granule/file-level search in the mid 1990s with EOSDIS-specific socket protocols and message formats. Since that time, the advent of several standards has helped to simplify EOSDIS federated search, beginning with HTTP as the transfer protocol. Most recently, OpenSearch (www.opensearch.org) was employed for the EOS Clearinghouse (ECHO), based on a set of conventions that had been developed within the Earth Science Information Partners (ESIP) Federation. The ECHO OpenSearch API has evolved to encompass the ESIP RFC and the Open Geospatial Consortium (OGC) Open Search standard. Uptake of the ECHO Open Search API has been significant and has made ECHO accessible to client developers that found the previous ECHO SOAP API and current REST API too complex. Client adoption of the OpenSearch API appears to be largely driven by the simplicity of the OpenSearch convention. This simplicity is thus important to retain as the standard and convention evolve. For example, ECHO metrics indicate that the vast majority of ECHO users favor the following search criteria when using the REST API, - Spatial - bounding box, polygon, line and point - Temporal - start and end time - Keywords - free text Fewer than 10% of searches use additional constraints, particularly those requiring a controlled vocabulary, such as instrument, sensor, etc. This suggests that ongoing standardization efforts around OpenSearch usage for Earth Observation data may be more productive if oriented toward improving support for the Spatial, Temporal and Keyword search aspects. Areas still requiring improvement include support of - Concrete requirements for keyword constraints - Phrasal search for keyword constraints - Temporal constraint relations - Terminological symmetry between search URLs and response documents for both temporal and spatial terms - Best practices for both servers and clients. Over the past year we have seen several ongoing efforts to further standardize Open Search in the earth science domain such as, - Federation of Earth Science Information Partners (ESIP) - Open Geospatial Consortium (OGC) - Committee on Earth Observation Satellites (CEOS)

Library API for Z-Order Memory Layout

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

Bethel, E. Wes

This library provides a simple-to-use API for implementing an altnerative to traditional row-major order in-memory layout, one based on a Morton- order space filling curve (SFC) , specifically, a Z-order variant of the Morton order curve. The library enables programmers to, after a simple initialization step, to convert a multidimensional array from row-major to Z- order layouts, then use a single, generic API call to access data from any arbitrary (i,j,k) location from within the array, whether it it be stored in row- major or z-order format. The motivation for using a SFC in-memory layout is for improved spatial locality,more » which results in increased use of local high speed cache memory. The basic idea is that with row-major order layouts, a data access to some location that is nearby in index space is likely far away in physical memory, resulting in poor spatial locality and slow runtime. On the other hand, with a SFC-based layout, accesses that are nearby in index space are much more likely to also be nearby in physical memory, resulting in much better spatial locality, and better runtime performance. Numerous studies over the years have shown significant runtime performance gains are realized by using a SFC-based memory layout compared to a row-major layout, sometimes by as much as 50%, which result from the better use of the memory and cache hierarchy that are attendant with a SFC-based layout (see, for example, [Beth2012]). This library implementation is intended for use with codes that work with structured, array-based data in 2 or 3 dimensions. It is not appropriate for use with unstructured or point-based data.« less

Pharmaceutical Cocrystals: New Solid Phase Modification Approaches for the Formulation of APIs

PubMed Central

Karagianni, Anna; Kachrimanis, Kyriakos

2018-01-01

Cocrystals can be used as an alternative approach based on crystal engineering to enhance specific physicochemical and biopharmaceutical properties of active pharmaceutical ingredients (APIs) when the approaches to salt or polymorph formation do not meet the expected targets. In this article, an overview of pharmaceutical cocrystals will be presented, with an emphasis on the intermolecular interactions in cocrystals and the methods for their preparation. Furthermore, cocrystals of direct pharmaceutical interest, along with their in vitro properties and available in vivo data and characterization techniques are discussed, highlighting the potential of cocrystals as an attractive route for drug development. PMID:29370068

Research on e-commerce transaction networks using multi-agent modelling and open application programming interface

NASA Astrophysics Data System (ADS)

Piao, Chunhui; Han, Xufang; Wu, Harris

2010-08-01

We provide a formal definition of an e-commerce transaction network. Agent-based modelling is used to simulate e-commerce transaction networks. For real-world analysis, we studied the open application programming interfaces (APIs) from eBay and Taobao e-commerce websites and captured real transaction data. Pajek is used to visualise the agent relationships in the transaction network. We derived one-mode networks from the transaction network and analysed them using degree and betweenness centrality. Integrating multi-agent modelling, open APIs and social network analysis, we propose a new way to study large-scale e-commerce systems.

OSCAR API for Real-Time Low-Power Multicores and Its Performance on Multicores and SMP Servers

NASA Astrophysics Data System (ADS)

Kimura, Keiji; Mase, Masayoshi; Mikami, Hiroki; Miyamoto, Takamichi; Shirako, Jun; Kasahara, Hironori

OSCAR (Optimally Scheduled Advanced Multiprocessor) API has been designed for real-time embedded low-power multicores to generate parallel programs for various multicores from different vendors by using the OSCAR parallelizing compiler. The OSCAR API has been developed by Waseda University in collaboration with Fujitsu Laboratory, Hitachi, NEC, Panasonic, Renesas Technology, and Toshiba in an METI/NEDO project entitled "Multicore Technology for Realtime Consumer Electronics." By using the OSCAR API as an interface between the OSCAR compiler and backend compilers, the OSCAR compiler enables hierarchical multigrain parallel processing with memory optimization under capacity restriction for cache memory, local memory, distributed shared memory, and on-chip/off-chip shared memory; data transfer using a DMA controller; and power reduction control using DVFS (Dynamic Voltage and Frequency Scaling), clock gating, and power gating for various embedded multicores. In addition, a parallelized program automatically generated by the OSCAR compiler with OSCAR API can be compiled by the ordinary OpenMP compilers since the OSCAR API is designed on a subset of the OpenMP. This paper describes the OSCAR API and its compatibility with the OSCAR compiler by showing code examples. Performance evaluations of the OSCAR compiler and the OSCAR API are carried out using an IBM Power5+ workstation, an IBM Power6 high-end SMP server, and a newly developed consumer electronics multicore chip RP2 by Renesas, Hitachi and Waseda. From the results of scalability evaluation, it is found that on an average, the OSCAR compiler with the OSCAR API can exploit 5.8 times speedup over the sequential execution on the Power5+ workstation with eight cores and 2.9 times speedup on RP2 with four cores, respectively. In addition, the OSCAR compiler can accelerate an IBM XL Fortran compiler up to 3.3 times on the Power6 SMP server. Due to low-power optimization on RP2, the OSCAR compiler with the OSCAR API achieves a maximum power reduction of 84% in the real-time execution mode.

The effect of various deformation processes on the corrosion behavior of casing and tubing carbon steels in sweet environment

NASA Astrophysics Data System (ADS)

Elramady, Alyaa Gamal

The aim of this research project is to correlate the plastic deformation and mechanical instability of casing steel materials with corrosion behavior and surface change, in order to identify a tolerable degree of deformation for casing steel materials. While the corrosion of pipeline and casing steels has been investigated extensively, corrosion of these steels in sweet environments with respect to plastic deformation due to bending, rolling, autofrettage, or handling needs more investigation. Downhole tubular expansion of pipes (casings) is becoming standard practice in the petroleum industry to repair damaged casings, shutdown perforations, and ultimately achieve mono-diameter wells. Tubular expansion is a cold-drawing metal forming process, which consists of running conical mandrels through casings either mechanically using a piston or hydraulically by applying a back pressure. This mechanism subjects the pipes to large radial plastic deformations of up to 30 pct. of the inner diameter. It is known that cold-working is a way of strengthening materials such as low carbon steel, but given that this material will be subjected to corrosive environments, susceptibility to stress corrosion cracking (SCC) should be investigated. This research studies the effect of cold-work, in the form of cold-rolling and cold-expansion, on the surface behavior of API 5CT steels when it is exposed to a CO2-containing environment. Cold-work has a pronounced influence on the corrosion behavior of both API 5CT K55 and P110 grade steels. The lowest strength grade steel, API 5CT K55, performed poorly in a corrosive environment in the slow strain rate test. The ductile material exhibited the highest loss in strength and highest susceptibility to stress corrosion cracking in a CO 2-containing environment. The loss in strength declined with cold-rolling, which can be ascribed to the surface compressive stresses induced by cold-work. On the other hand, API 5CT P110 grade steels showed higher susceptibility to SCC when they were cold-rolled and cold-expanded. The research found that surface compressive stresses have an effect on the SCC behavior of casing and tubing steels. The CO2 corrosion behavior and atomic processes at the corroding interface were investigated at laboratory temperature using electrochemical techniques. Cold-work was found to have an influence on the corrosion behavior of both API 5CT K55 and P110 grade steels. These behaviors were found to be material and process dependent. Surface evaluation techniques such as field emission scanning electron microscope (FE-SEM) and X-ray diffraction (XRD) analysis did not detect formation of a protective scale. X-ray diffraction and X-ray photoelectron spectroscopy (XPS) analysis both detected the appearance of a scale that was traced back to magnetite.

Component-resolved evaluation of the content of major allergens in therapeutic extracts for specific immunotherapy of honeybee venom allergy

PubMed Central

Blank, Simon; Etzold, Stefanie; Darsow, Ulf; Schiener, Maximilian; Eberlein, Bernadette; Russkamp, Dennis; Wolf, Sara; Graessel, Anke; Biedermann, Tilo; Ollert, Markus; Schmidt-Weber, Carsten B.

2017-01-01

ABSTRACT Allergen-specific immunotherapy is the only curative treatment of honeybee venom (HBV) allergy, which is able to protect against further anaphylactic sting reactions. Recent analyses on a molecular level have demonstrated that HBV represents a complex allergen source that contains more relevant major allergens than formerly anticipated. Moreover, allergic patients show very diverse sensitization profiles with the different allergens. HBV-specific immunotherapy is conducted with HBV extracts which are derived from pure venom. The allergen content of these therapeutic extracts might differ due to natural variations of the source material or different down-stream processing strategies of the manufacturers. Since variations of the allergen content of therapeutic HBV extracts might be associated with therapeutic failure, we adressed the component-resolved allergen composition of different therapeutic grade HBV extracts which are approved for immunotherapy in numerous countries. The extracts were analyzed for their content of the major allergens Api m 1, Api m 2, Api m 3, Api m 5 and Api m 10. Using allergen-specific antibodies we were able to demonstrate the underrepresentation of relevant major allergens such as Api m 3, Api m 5 and Api m 10 in particular therapeutic extracts. Taken together, standardization of therapeutic extracts by determination of the total allergenic potency might imply the intrinsic pitfall of losing information about particular major allergens. Moreover, the variable allergen composition of different therapeutic HBV extracts might have an impact on therapy outcome and the clinical management of HBV-allergic patients with specific IgE to particular allergens. PMID:28494206

API2-MALT1 oncoprotein promotes lymphomagenesis via unique program of substrate ubiquitination and proteolysis

PubMed Central

Rosebeck, Shaun; Lim, Megan S; Elenitoba-Johnson, Kojo S J; McAllister-Lucas, Linda M; Lucas, Peter C

2016-01-01

Lymphoma of mucosa-associated lymphoid tissue (MALT lymphoma) is the most common extranodal B cell tumor and accounts for 8% of non-Hodgkin’s lymphomas. Gastric MALT lymphoma is the best-studied example and is a prototypical neoplasm that occurs in the setting of chronic inflammation brought on by persistent infection or autoimmune disease. Cytogenetic abnormalities are commonly acquired during the course of disease and the most common is chromosomal translocation t(11;18)(q21;q21), which creates the API2-MALT1 fusion oncoprotein. t(11;18)-positive lymphomas can be clinically aggressive and have a higher rate of dissemination than t(11;18)-negative tumors. Many cancers, including MALT lymphomas, characteristically exhibit deregulated over-activation of cellular survival pathways, such as the nuclear factor-κB (NF-κB) pathway. Molecular characterization of API2-MALT1 has revealed it to be a potent activator of NF-κB, which is required for API2-MALT1-induced cellular transformation, however the mechanisms by which API2-MALT1 exerts these effects are only recently becoming apparent. The API2 moiety of the fusion binds tumor necrosis factor (TNF) receptor associated factor (TRAF) 2 and receptor interacting protein 1 (RIP1), two proteins essential for TNF receptor-induced NF-κB activation. By effectively mimicking ligand-bound TNF receptor, API2-MALT1 promotes TRAF2-dependent ubiquitination of RIP1, which then acts as a scaffold for nucleating and activating the canonical NF-κB machinery. Activation occurs, in part, through MALT1 moiety-dependent recruitment of TRAF6, which can directly modify NF-κB essential modulator, the principal downstream regulator of NF-κB. While the intrinsic MALT1 protease catalytic activity is dispensable for this canonical NF-κB signaling, it is critical for non-canonical NF-κB activation. In this regard, API2-MALT1 recognizes NF-κB inducing kinase (NIK), the essential upstream regulator of non-canonical NF-κB, and cleaves it to generate a stable, constitutively active fragment. Thus, API2-MALT1 harnesses multiple unique pathways to achieve deregulated NF-κB activation. Emerging data from our group and others have also detailed additional gain-of-function activities of API2-MALT1 that extend beyond NF-κB activation. Specifically, API2-MALT1 recruits and subverts multiple other signaling factors, including LIM domain and actin-binding protein 1 (LIMA1) and Smac/DIABLO. Like NIK, LIMA1 represents a unique substrate for API2-MALT1 protease activity, but unlike NIK, its cleavage sets in motion a major NF-κB-independent pathway for promoting oncogenesis. In this review, we highlight the most recent results characterizing these unique and diverse gain-of-function activities of API2-MALT1 and how they contribute to lymphomagenesis. PMID:26981201

Nosema ceranae, a newly identified pathogen of Apis mellifera in the U.S. and Asia

USDA-ARS?s Scientific Manuscript database

Nosemosis (Nosema disease) is one of the most serious and prevalent adult honey bee diseases worldwide. For years, Nosema apis was thought to be the only microsporidia infecting domestic bee colonies. However, recently it was discovered that N. ceranae could jump from Asian honey bees (Apis cerana...

Targeted Information Dissemination

DTIC Science & Technology

2008-03-01

SETUP, RESULTS AND PERFORMANCE ANALYSIS .......................................... 36 APPENDIX C: TID API SPECIFICATION...are developed using FreePastry1. FreePastry provides an API for a structured P2P overlay network. Information Routing and address resolution is...the TID architecture to demonstrate its key features. TID interface API specifications are described in Appendix C. RSS feeds were used to obtain

30 CFR 250.114 - How must I install and operate electrical equipment?

Code of Federal Regulations, 2012 CFR

2012-07-01

... their facilities. (a) You must classify all areas according to API RP 500, Recommended Practice for... 1 and Division 2, or API RP 505, Recommended Practice for Classification of Locations for Electrical... electrical systems according to API RP 14F, Recommended Practice for Design and Installation of Electrical...

49 CFR 195.307 - Pressure testing aboveground breakout tanks.

Code of Federal Regulations, 2013 CFR

2013-10-01

... aboveground breakout tanks. (a) For aboveground breakout tanks built into API Specification 12F and first placed in service after October 2, 2000, pneumatic testing must be in accordance with section 5.3 of API Specification 12 F (incorporated by reference, see § 195.3). (b) For aboveground breakout tanks built to API...

49 CFR 195.405 - Protection against ignitions and safe access/egress involving floating roofs.

Code of Federal Regulations, 2010 CFR

2010-10-01

... accordance with API Recommended Practice 2003, unless the operator notes in the procedural manual (§ 195.402(c)) why compliance with all or certain provisions of API Recommended Practice 2003 is not necessary... removed from service for cleaning) are addressed in API Publication 2026. After October 2, 2000, the...

30 CFR 250.114 - How must I install and operate electrical equipment?

Code of Federal Regulations, 2011 CFR

2011-07-01

... structures, and their facilities. (a) You must classify all areas according to API RP 500, Recommended... Class I, Division 1 and Division 2, or API RP 505, Recommended Practice for Classification of Locations... according to API RP 14F, Recommended Practice for Design and Installation of Electrical Systems for Fixed...

30 CFR 250.114 - How must I install and operate electrical equipment?

Code of Federal Regulations, 2014 CFR

2014-07-01

... their facilities. (a) You must classify all areas according to API RP 500, Recommended Practice for... 1 and Division 2, or API RP 505, Recommended Practice for Classification of Locations for Electrical... electrical systems according to API RP 14F, Recommended Practice for Design and Installation of Electrical...

49 CFR 195.405 - Protection against ignitions and safe access/egress involving floating roofs.

Code of Federal Regulations, 2011 CFR

2011-10-01

... accordance with API Recommended Practice 2003, unless the operator notes in the procedural manual (§ 195.402(c)) why compliance with all or certain provisions of API Recommended Practice 2003 is not necessary... removed from service for cleaning) are addressed in API Publication 2026. After October 2, 2000, the...

49 CFR 195.405 - Protection against ignitions and safe access/egress involving floating roofs.

Code of Federal Regulations, 2012 CFR

2012-10-01

... accordance with API Recommended Practice 2003, unless the operator notes in the procedural manual (§ 195.402(c)) why compliance with all or certain provisions of API Recommended Practice 2003 is not necessary... removed from service for cleaning) are addressed in API Publication 2026. After October 2, 2000, the...

49 CFR 195.405 - Protection against ignitions and safe access/egress involving floating roofs.

Code of Federal Regulations, 2013 CFR

2013-10-01

... accordance with API Recommended Practice 2003, unless the operator notes in the procedural manual (§ 195.402(c)) why compliance with all or certain provisions of API Recommended Practice 2003 is not necessary... removed from service for cleaning) are addressed in API Publication 2026. After October 2, 2000, the...

49 CFR 195.307 - Pressure testing aboveground breakout tanks.

Code of Federal Regulations, 2012 CFR

2012-10-01

... aboveground breakout tanks. (a) For aboveground breakout tanks built into API Specification 12F and first placed in service after October 2, 2000, pneumatic testing must be in accordance with section 5.3 of API Specification 12 F (incorporated by reference, see § 195.3). (b) For aboveground breakout tanks built to API...

49 CFR 195.405 - Protection against ignitions and safe access/egress involving floating roofs.

Code of Federal Regulations, 2014 CFR

2014-10-01

... accordance with API Recommended Practice 2003, unless the operator notes in the procedural manual (§ 195.402(c)) why compliance with all or certain provisions of API Recommended Practice 2003 is not necessary... removed from service for cleaning) are addressed in API Publication 2026. After October 2, 2000, the...