Nanoinformatics for environmental health and biomedicine

• Rong Liu and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 2449–2451, doi:10.3762/bjnano.6.253

• properties, toxicity behavior, processing information, production levels, environmental releases, and more. Accordingly advanced informatics techniques are urgently required for the collection and curation, management (e.g., achieving and sharing), analysis and modeling of the large amount of data involved

An adapted Coffey model for studying susceptibility losses in interacting magnetic nanoparticles

• Mihaela Osaci and
• Matteo Cacciola

Beilstein J. Nanotechnol. 2015, 6, 2173–2182, doi:10.3762/bjnano.6.223

• Mihaela Osaci Matteo Cacciola “Politehnica” University of Timisoara, Department of Electrical Engineering and Industrial Informatics, Piata Victoriei Nr. 2, 300006 Timisoara, jud. Timis, Romania University “Mediterranea” of Reggio Calabria, DICEAM, Via Graziella Feo di Vito, I-89100 Reggio

An ISA-TAB-Nano based data collection framework to support data-driven modelling of nanotoxicology

• Richard L. Marchese Robinson,
• Mark T. D. Cronin,
• Andrea-Nicole Richarz and
• Robert Rallo

Beilstein J. Nanotechnol. 2015, 6, 1978–1999, doi:10.3762/bjnano.6.202

• entry of data into (web-based) searchable databases may not be possible for domain experts (e.g., nanotoxicologists in experimental labs) with little or no informatics support. These researchers may not have their own, in-house database systems and data entry to a third party database at the point of

Predicting cytotoxicity of PAMAM dendrimers using molecular descriptors

• David E. Jones,
• Hamidreza Ghandehari and
• Julio C. Facelli

Beilstein J. Nanotechnol. 2015, 6, 1886–1896, doi:10.3762/bjnano.6.192

• David E. Jones Hamidreza Ghandehari Julio C. Facelli Department of Biomedical Informatics, University of Utah, Salt Lake City, UT 84112, USA Department of Bioengineering, University of Utah, Salt Lake City, UT 84112, USA Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah

Nanocuration workflows: Establishing best practices for identifying, inputting, and sharing data to inform decisions on nanomaterials

• Christina M. Powers,
• Karmann A. Mills,
• Stephanie A. Morris,
• Fred Klaessig,
• Sharon Gaheen,
• Nastassja Lewinski and
• Christine Ogilvie Hendren

Beilstein J. Nanotechnol. 2015, 6, 1860–1871, doi:10.3762/bjnano.6.189

• nanoscience to compare and integrate information across diverse fields of study through informatics (i.e., nanoinformatics). This paper is one in a series of articles on the data curation process in nanoinformatics (nanocuration). Other articles in this series discuss key aspects of nanocuration (temporal

• groups) and providing nanocuration resources (e.g., training) will likely prove crucial for the wider application of nanocuration workflows in the scientific community. Keywords: curation; informatics; nanoinformatics; nanomaterials; workflows; Introduction A tremendous growth in resources and tools to

• in order to describe current practices. Articles in this series are developed by the Nanomaterials Data Curation Initiative (NDCI), which is part of the National Cancer Informatics Program Nanotechnology Working Group [1]. Other articles in this series discuss several key aspects of nanocuration

The Nanomaterial Data Curation Initiative: A collaborative approach to assessing, evaluating, and advancing the state of the field

• Christine Ogilvie Hendren,
• Christina M. Powers,
• Mark D. Hoover and
• Stacey L. Harper

Beilstein J. Nanotechnol. 2015, 6, 1752–1762, doi:10.3762/bjnano.6.179

• School of Chemical, Biological and Environmental Engineering, Oregon State University, Corvallis, OR, USA 10.3762/bjnano.6.179 Abstract The Nanomaterial Data Curation Initiative (NDCI), a project of the National Cancer Informatics Program Nanotechnology Working Group (NCIP NanoWG), explores the critical

• aspect of data curation within the development of informatics approaches to understanding nanomaterial behavior. Data repositories and tools for integrating and interrogating complex nanomaterial datasets are gaining widespread interest, with multiple projects now appearing in the US and the EU. Even in

• sharing and to develop and apply complementary approaches to collect, manage and share data in ways that can support those purposes. Community focus on building effective nanoinformatics approaches The need for collaborative and dedicated attention to informatics in the nanomaterial community was a focal

Analyzing collaboration networks and developmental patterns of nano-enabled drug delivery (NEDD) for brain cancer

• Ying Huang,
• Jing Ma,
• Alan L. Porter,
• Seokbeom Kwon and
• Donghua Zhu

Beilstein J. Nanotechnol. 2015, 6, 1666–1676, doi:10.3762/bjnano.6.169

• related fields. It is vital in interdisciplinary arenas and nano-bio-informatics can bolster intelligence concerning advances and potential collaborators. “R&D landscaping” to understand collaboration and developmental patterns can offer global-level insights [12]. This paper aims to support policy-makers

• challenges, and curing brain cancer is a high potential application of NEDD that is worth of more exploration. Exploring nano biomedicine research from the respective of social science causes us great interest. Literature informatics, such as our multi-tier R&D landscaping, can help inform science policy

Experiences in supporting the structured collection of cancer nanotechnology data using caNanoLab

• Stephanie A. Morris,
• Sharon Gaheen,
• Michal Lijowski,
• Mervi Heiskanen and
• Juli Klemm

Beilstein J. Nanotechnol. 2015, 6, 1580–1593, doi:10.3762/bjnano.6.161

• , Frederick, MD, 21701, USA Essential Software, Inc., 9024 Mistwood Drive, Potomac, MD, 20854, USA Center for Biomedical Informatics and Information Technology, National Cancer Institute/NIH, 9609 Medical Center Drive, Rockville, MD, 20850, USA 10.3762/bjnano.6.161 Abstract The cancer Nanotechnology

• Cancer Institute’s (NCI) Office of Cancer Nanotechnology Research and Center for Biomedical Informatics and Information Technology to address the characterization requirements for federal regulatory review of nanomaterial-based investigational new drugs, diagnostic devices, and imaging agents [11][12

• needed based on the purpose of the study, which may vary based on the nanotechnology application [19]. Considering these issues, caNanoLab and other nanomaterial databases require input and support from users including informatics experts, nanotechnologists, biologists, and clinicians to better

Using natural language processing techniques to inform research on nanotechnology

• Nastassja A. Lewinski and
• Bridget T. McInnes

Beilstein J. Nanotechnol. 2015, 6, 1439–1449, doi:10.3762/bjnano.6.149

• and their associated physico-chemical properties, performance, exposure scenarios, and biological effects. In this paper, we review the different informatics methods that have been applied to patent mining, nanomaterial/device characterization, nanomedicine, and environmental risk assessment. Nine

• online repositories to broaden participation in nanoinformatics. Keywords: data mining; informatics; name entity recognition; nano-informatics; nanoparticles; nanotechnology; nanotoxicity; natural language processing; text mining; Introduction Nanotechnology may still be considered a relatively new

• language processing methods are applied, and (2) experimental data to which data modeling methods, such as those used in HDAT and NanoMiner, are applied [5][6]. Despite being a largely overlooked area of informatics, several reviews have been published that list the different databases and tools currently

Tattoo ink nanoparticles in skin tissue and fibroblasts

• Colin A. Grant,
• Peter C. Twigg,
• Richard Baker and
• Desmond J. Tobin

Beilstein J. Nanotechnol. 2015, 6, 1183–1191, doi:10.3762/bjnano.6.120

• Colin A. Grant Peter C. Twigg Richard Baker Desmond J. Tobin Advanced Materials Engineering, Faculty of Engineering and Informatics, University of Bradford, Bradford, BD7 1DP, United Kingdom Centre for Skin Sciences, Faculty of Life Sciences, University of Bradford, Bradford, BD7 1DP, United

Probing fibronectin–antibody interactions using AFM force spectroscopy and lateral force microscopy

• Andrzej J. Kulik,
• Małgorzata Lekka,
• Kyumin Lee,
• Grazyna Pyka-Fościak and
• Wieslaw Nowak

Beilstein J. Nanotechnol. 2015, 6, 1164–1175, doi:10.3762/bjnano.6.118

• Kraków, Poland Department of Histology, Jagiellonian University Medical College, Kopernika 7, 31-034 Kraków, Poland, Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziądzka 5/7, 87-100 Toruń, Poland 10.3762/bjnano.6.118 Abstract The first

Interaction of electromagnetic radiation in the 20–200 GHz frequency range with arrays of carbon nanotubes with ferromagnetic nanoparticles

• Agylych Atdayev,
• Alexander L. Danilyuk and
• Serghej L. Prischepa

Beilstein J. Nanotechnol. 2015, 6, 1056–1064, doi:10.3762/bjnano.6.106

• Agylych Atdayev Alexander L. Danilyuk Serghej L. Prischepa Belarusian State University of Informatics and Radioelectronics, P. Browka St. 6, 220013 Minsk, Belarus 10.3762/bjnano.6.106 Abstract The interaction of electromagnetic radiation with a magnetic nanocomposite based on carbon nanotubes

Nanoscopic surfactant behavior of the porin MspA in aqueous media

• Ayomi S. Perera,
• Hongwang Wang,
• Tej B. Shrestha,
• Deryl L. Troyer and
• Stefan H. Bossmann

Beilstein J. Nanotechnol. 2013, 4, 278–284, doi:10.3762/bjnano.4.30

• ) were adapted from [18] using the UCSF Chimera software. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco (supported by NIGMS P41-GM103311) [19]. Hydrodynamic diameter of MspA aggregates as a function of temperature