11,764 Works

Curating and Sharing Structures.pptCurating and sharing structures and spectra for the environmental community

Antony Williams &
The increasing popularity of high mass accuracy non-target mass spectrometry methods has yielded extensive identification efforts based on spectral and chemical compound databases in the environmental community and beyond. Increasingly, new methods are relying on open data resources. Candidate structures are often retrieved with either exact mass or molecular formula from large resources such as PubChem, ChemSpider or the EPA CompTox Chemistry Dashboard. Smaller, selective lists of chemicals (also called “suspect lists”) can be used...

Using the US EPA’s CompTox Chemistry Dashboard for structure identification and non-targeted analyses

Antony Williams
High resolution mass spectrometry (HRMS) and non-targeted analysis (NTA) are advancing the identification of emerging contaminants in environmental matrices, improving the means by which exposure analyses can be conducted. However, confidence in structure identification of unknowns in NTA presents challenges to analytical chemists. Structure identification requires integration of complementary data types such as reference databases, fragmentation prediction tools, and retention time prediction models. The goal of this research is to optimize and implement structure identification...

US EPA CompTox Chemistry Dashboard as a source of data to fill data gaps for chemical sources of risk

Antony Williams, Imran Shah, Grace Patlewicz, John Wambaugh, Ann Richard, Richard Judson, Chris Grulke & Todd Martin
Chemical risk assessment is both time-consuming and difficult because it requires the assembly of data for chemicals generally distributed across multiple sources. The US EPA CompTox Chemistry Dashboard is a publicly accessible web-based application providing access to various data streams on ~760,000 chemical substances. These data include experimental and predicted physicochemical property data, bioassay screening data associated with the ToxCast program, consumer product and functional use information and a myriad of related data of value...

MOESM3 of Nanoparticles engineered to bind cellular motors for efficient delivery

Inmaculada Dalmau-Mena, Pablo Pino, Beatriz Pelaz, Miguel Cuesta-Geijo, Inmaculada Galindo, María Moros, Jesús Fuente &
Additional file 3: Movie 2. Intracellular movement of NPs linear trajectories. This movie displays a Vero cell incubated with Au@DynPro at 0.2 mg/ml during 1.5 h showing linear and stable tracks of directed motion in the perinuclear area. The time lapse covers 40 s at a rate of 3 frames/s.

RCCPII eConversations: Virtual Platforms for Research and Collaboration

Anelda Van Der Walt & Erika Mias
This presentation was delivered during a 90 minute online RCCPII eConversation session where the speakers shared tips and tricks as well as best practices for using a variety of virtual platforms for online collaboration in academic institutions. The presentation is split into two parts: the first focuses on tools for general use and the second on those more applicable in a research setting.These online sessions are part of the Rural Campuses Connection Project II (RCCPII)...

Visualization 1 Simulation of PSF as a function of displacement of lens L2.mov

Simulation of PSF as a function of displacement of lens L2. Displacing Lens L2 (e.g., changing relative displacement D from – 20 mm to 20 mm) alters the amplitude and phase distribution on the back focal plane of the objective, axial, and lateral PSFs. Same parameters as described in caption of Fig. 1 were used for simulation.

Additional file 5: of UDiTaSâ ˘, a genome editing detection method for indels and genome rearrangements

Georgia Giannoukos, Dawn Ciulla, Eugenio Marco, Hayat Abdulkerim, Luis Barrera, Anne Bothmer, Vidya Dhanapal, Sebastian Gloskowski, Hariharan Jayaram, Morgan Maeder, Maxwell Skor, , Vic Myer & Christopher Wilson
Figure S4. Binomial power calculation applied to UDiTaS. A simulated binomial distribution, plotting editing frequency (e.g.: probability of success) vs. number of unique molecular identifiers (e.g.: trials) for a given number of expected observations (1, 2, or 3). Graphs on the left are 95% confidence and right 99% confidence. (PPTX 86Â kb)

First-in-Man Large-Field Intravascular Ultrasound-Guided Transcatheter Aortic Valve Replacement

Massoud A. Leesar, , Mark F. Sasse, , Satinder Singh & James E. Davies
First-in-Man Large-Field Intravascular Ultrasound-Guided Transcatheter Aortic Valve Replacement

Collaborations Workshop 2018 - Lightning talk - Becky Arnold

Becky Arnold
Presentation during Collaborations Workshop 2018, https://www.software.ac.uk/cw18/.

Collaborations Workshop 2018 - Lightning talk - Sam Cox

Sam Cox
Presentation during Collaborations Workshop 2018, https://www.software.ac.uk/cw18/.

Collaborations Workshop 2018 - Lightning talk - Martin O'Reilly

Martin O'Reilly
Presentation during Collaborations Workshop 2018, https://www.software.ac.uk/cw18/.

Are we interoperable yet?

Adrian-Tudor Panescu
This is a talk first given at the Software Sustainability Institute Collaborations Workshop 2018 (https://www.software.ac.uk/cw18) on interoperability across the scientific research infrastructure.

Sharing chemical structures with peer-reviewed publications. Are we there yet?

Antony Williams
In the domain of chemistry one of the greatest benefits to publishing research is that data can be shared. Unfortunately, the vast majority of chemical structure data associated with scientific publications remain locked up in document form, primarily in PDF files or trapped on webpages. Despite the explosive growth of online chemical databases and the overall maturity of cheminformatics platforms, many barriers stifle the exchange of chemical structures via publications. These challenges include incomplete support...

Overview of open resources to support automated structure verification and elucidation

Antony Williams & Emma Schymanski
Cheminformatics methods form an essential basis for providing analytical scientists with access to data, algorithms and workflows. There are an increasing number of free online databases (compound databases, spectral libraries, data repositories) and a rich collection of software approaches that can be used to support automated structure verification and elucidation, specifically for Nuclear Magnetic Resonance (NMR) and Mass Spectrometry (MS). This presentation will provide an overview of freely available data, tools, databases and approaches available...

New developments in delivering public access to data from the National Center for Computational Toxicology at the EPA

Antony Williams
Researchers at EPA’s National Center for Computational Toxicology integrate advances in biology, chemistry, and computer science to examine the toxicity of chemicals and help prioritize chemicals for further research based on potential human health risks. The goal of this research program is to quickly evaluate thousands of chemicals, but at a much reduced cost and shorter time frame relative to traditional approaches. The data generated by the Center includes characterization of thousands of chemicals across...

Markmið og gerð spurningalistanna. Rannsóknar- og þróunarverkefnið SamGETA

Svava Pétursdóttir, Allyson Macdonald, Svanborg R. Jónsdóttir, Auður Pálsdóttir &
In Icelandic
About how the questionnaries was developed in the researchproject SamGETA

The citation (APA style)
Svava Pétursdóttir, Svanborg R. Jónsdóttir, Auður Pálsdóttir, Allyson Macdonald og Sigurbjörg Jóhannesdóttir. (2017, 6. október). Markmið og gerð spurningalistanna. Erindi í málstofu SamGETA - Um trú kennara á sameiginlegri getu á nýjum sviðum. Menntakvika, Menntavísindasvið Háskóla Íslands.

Visualization_3.avi

Ireneusz Grulkowski, Silvestre Manzanera, , Franciszek Sobczuk, Karol Karnowski & Pablo Artal
Enhanced 3-D visualization of anterior vitreous opacifications

movieS1.avi

This video provides a visualization of the laser’s raster scanning of the visible wall, and the occluder’s resulting shadow on the hidden wall.

A Qualitative Study of Open Educational Practice using Jupyter Notebooks

Lorena A. Barba
2018 Open Education Global Conference
Research efforts in the last decade have focused on the effect on student outcomes from using Open Educational Resources (OER). We are interested in whether (some) OER may also influence students in their attitudes and capacities for collaboration, community involvement, and open practices. The aim of our study is to discover how a new OER medium, Jupyter Notebooks, may (or may not) impact attitudes of undergraduate engineering majors toward sharing and...

SI2-SSE: GenApp - A Transformative Generalized Application Cyberinfrastructure

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GenApp, a Generalized Application Framework [https://genapp.rocks], is a framework for rapidly building and deploying applications to an extensible variety of targets including web-based science gateways. GenApp works by building targets from a collection of definition files. An existing program can be brought into GenApp by writing a definition file and wrapping or modifying the program to accept inputs and produce ou tputsas defined. GenApp was developed to support the needs of the SI2-CHE CCP-SAS project...

MOESM1 of Consistent map building in petrochemical complexes for firefighter robots using SLAM based on GPS and LIDAR

Abu Shamsudin, Kazunori Ohno, Ryunosuke Hamada, Shotaro Kojima, Thomas Westfechtel, Takahiro Suzuki, Yoshito Okada, Satoshi Tadokoro, Jun Fujita & Hisanori Amano
Additional file 1. A supplement to this paper is a movie on the Fast-SLAM 2.0 based on GPS and LIDAR in a petrochemical complexes.

Additional file 2: of Lipid accumulation in human breast cancer cells injured by iron depletors

Maida De Bortoli, Elena Taverna, Elisa Maffioli, Patrizia Casalini, Francesco Crisafi, Vikas Kumar, Claudio Caccia, Dario Polli, Gabriella Tedeschi & Italia Bongarzone
FACS analysis of cell cycle. (PPTX 200 kb)

Audio File S3 Novel Human sounds from Imitation of novel conspecific and human speech sounds in the killer whale (Orcinus orca)

José Z. Abramson, , Lino García, Fernando Colmenares, Francisco Aboitiz & Josep Call
Five randomly chosen examples for each sound: S3.4 ‘One Two’

Audio File S3 Novel Human sounds from Imitation of novel conspecific and human speech sounds in the killer whale (Orcinus orca)

José Z. Abramson, , Lino García, Fernando Colmenares, Francisco Aboitiz & Josep Call
Five randomly chosen examples for each sound: S3.1‘Hello’

Audio File S3 Novel Human sounds;RAW DATA from Imitation of novel conspecific and human speech sounds in the killer whale (Orcinus orca)

José Z. Abramson, , Lino García, Fernando Colmenares, Francisco Aboitiz & Josep Call
Five randomly chosen examples for each sound: S3.5 ‘One Two Three’

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