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

• metadata, data completeness, database integration), while the focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository. In particular, the article discusses: 1) the rationale and importance of a defined workflow in

• (temporal metadata, data completeness, database integration), while the specific focus of this article is on the nanocuration workflow, or the process of identifying, inputting, and reviewing nanomaterial data in a data repository (Figure 1). Discussion i. Importance and relevance of the workflow to

• generate a large number of products and applications. Continuing the current tendency for each organization to maintain its own database with local interpretations of acceptable test protocols and data interpretation will impede the pace of innovation when organizations repeat work already done, but not

Metal hydrides: an innovative and challenging conversion reaction anode for lithium-ion batteries

• Luc Aymard,
• Yassine Oumellal and
• Jean-Pierre Bonnet

Beilstein J. Nanotechnol. 2015, 6, 1821–1839, doi:10.3762/bjnano.6.186

• the cell (Eeq) is: This calculation was applied for different binary and ternary hydrides used to represent the different intermetallic families. The HSC database [7] and literature data [8] were used to obtain the ΔfH, ΔfG and ΔfS values. I.2.1 Binary hydrides: Figure 2a shows the equilibrium

NanoE-Tox: New and in-depth database concerning ecotoxicity of nanomaterials

• Katre Juganson,
• Angela Ivask,
• Irina Blinova,
• Monika Mortimer and
• Anne Kahru

Beilstein J. Nanotechnol. 2015, 6, 1788–1804, doi:10.3762/bjnano.6.183

• database NanoE-Tox that is available as Supporting Information File 2. The database is based on existing literature on ecotoxicology of eight ENMs with different chemical composition: carbon nanotubes (CNTs), fullerenes, silver (Ag), titanium dioxide (TiO2), zinc oxide (ZnO), cerium dioxide (CeO2), copper

• oxide (CuO), and iron oxide (FeOx; Fe2O3, Fe3O4). Altogether, NanoE-Tox database consolidates data from 224 articles and lists altogether 1,518 toxicity values (EC50/LC50/NOEC) with corresponding test conditions and physico-chemical parameters of the ENMs as well as reported toxicity mechanisms and

• sensitive organism (data derived from three or more articles) the toxicity order was as follows: Ag > ZnO > CuO > CeO2 > CNTs > TiO2 > FeOx. We believe NanoE-Tox database contains valuable information for ENM environmental hazard estimation and development of models for predicting toxic potential of ENMs

Nanotechnology in the real world: Redeveloping the nanomaterial consumer products inventory

• Marina E. Vance,
• Todd Kuiken,
• Eric P. Vejerano,
• Sean P. McGinnis,
• Michael F. Hochella Jr.,
• David Rejeski and
• Matthew S. Hull

Beilstein J. Nanotechnol. 2015, 6, 1769–1780, doi:10.3762/bjnano.6.181

• environmental exposure data to complete life cycle assessments. There are inherent limitations to this type of database, but these modifications to the inventory addressed the majority of criticisms raised in published literature and in surveys of nanotechnology stakeholders and experts. The development of

• standardized methods and metrics for nanomaterial characterization and labelling in consumer products can lead to greater understanding between the key stakeholders in nanotechnology, especially consumers, researchers, regulators, and industry. Keywords: consumer products; database; inventory; nanoinformatics

• the CPI database [7]. Since the creation of the CPI, other nanotechnology-related inventories have been developed around the world. In 2006, a German company launched a freely accessible internet database of nanotechnology products [8]. The website associated with this database was not accessible at

The eNanoMapper database for nanomaterial safety information

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

Beilstein J. Nanotechnol. 2015, 6, 1609–1634, doi:10.3762/bjnano.6.165

• 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

How decision analysis can further nanoinformatics

• Matthew E. Bates,
• Sabrina Larkin,
• Jeffrey M. Keisler and
• Igor Linkov

Beilstein J. Nanotechnol. 2015, 6, 1594–1600, doi:10.3762/bjnano.6.162

• Information Library (NIL) is a database from the National Institute for Occupational Safety and Health (NIOSH) that aggregates the physical characteristics of nanomaterials for industrial users, researchers, and health professionals to access and share [7]. The NanoHub offers a collaborative workspace for

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

• Laboratory (caNanoLab) data portal is an online nanomaterial database that allows users to submit and retrieve information on well-characterized nanomaterials, including composition, in vitro and in vivo experimental characterizations, experimental protocols, and related publications. Initiated in 2006

• review, comparison, and re-use, with the ultimate goal of accelerating the translation of nanotechnology-based cancer therapeutics, diagnostics, and imaging agents to the clinic. In this paper, we will discuss challenges associated with developing a nanomaterial database and recognized needs for

• -based database that allows users to submit and retrieve information on highly described nanomaterials used in biomedicine. We provide an overview of caNanoLab functionality and the release of caNanoLab 2.0, which contains new features and enhancements that address some of the barriers to data sharing

Influence of surface chemical properties on the toxicity of engineered zinc oxide nanoparticles to embryonic zebrafish

• Zitao Zhou,
• Jino Son,
• Bryan Harper,
• Zheng Zhou and
• Stacey Harper

Beilstein J. Nanotechnol. 2015, 6, 1568–1579, doi:10.3762/bjnano.6.160

• of data variance, PCA effectively reduced the dimensions of the dataset with keeping most information. It eliminated the correlation between different independent variables by creating different linear combinations which are independent of each other [40]. PCA was conducted on the database that

• individual NP exposure dataset is comprised of results from experiments conducted at 8 exposure concentrations, thus the final matrix of the database was comprised of 136 rows and 8 columns (17 materials × 8 concentrations × 8 surface chemical properties). The first two principle components (PCs), whose

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

• database. Text extraction was conducted, with fuzzy logic used to cleanse the data. Fuzzy matching techniques were used to identify and combine similar entities. List Process, Matrix Process, Factor Analysis, Technology Group Clustering, and Concept Hierarchy were used in the framework to analyze the

• database. Multi-dimensional scaling was employed with a path erasing algorithm. The data presented focused on identifying leading countries, companies and inventors in the nanotechnology field. At the time of publication, the top three patenting institutions representing the top three patenting countries

Simulation tool for assessing the release and environmental distribution of nanomaterials

• Haoyang Haven Liu,
• Muhammad Bilal,
• Anastasiya Lazareva,
• Arturo Keller and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 938–951, doi:10.3762/bjnano.6.97

• interface for scenario design and results visualization, (2) MendNano, which is a fate and transport model for estimating environmental ENM concentrations, (3) lifecycle environmental assessment for release of nanomaterials (LearNano) model for estimating ENM release rates, (4) a parameter database, and (5

• ) a repository for building a library of scenarios and simulation cases. The RedNano graphical user interface (GUI) provides guidance for scenario design and parameter specification; the latter may be obtained from an integrated parameter database, input manually, or calculated by various submodels

• provided in standard numerical formats. Additionally, scenario input data as well as intermediary and final simulation results are stored in the scenario database. The RedNano integrated simulation tool was designed as a client–server web application using a standard web development environment (i.e., HTML

Morphological and structural characterization of single-crystal ZnO nanorod arrays on flexible and non-flexible substrates

• Omar F. Farhat,
• Mohd M. Halim,
• Mat J. Abdullah,
• Mohammed K. M. Ali and
• Nageh K. Allam

Beilstein J. Nanotechnol. 2015, 6, 720–725, doi:10.3762/bjnano.6.73

• ° corresponding to ZnO (002), revealing the preferentially oriented growth along the c-axis. All diffraction peaks are consistent with the wurtzite structure of ZnO [16], which can be indexed to a standard spectrum in the ICSD database (No. 01-079-0207). Additional broad and highly intense diffraction peaks were

Self-assembled anchor layers/polysaccharide coatings on titanium surfaces: a study of functionalization and stability

• Ognen Pop-Georgievski,
• Dana Kubies,
• Josef Zemek,
• Neda Neykova,
• Roman Demianchuk,
• Eliška Mázl Chánová,
• Miroslav Šlouf,
• Milan Houska and
• František Rypáček

Beilstein J. Nanotechnol. 2015, 6, 617–631, doi:10.3762/bjnano.6.63

• = 1.4714 ± 0.008, Bn = 13200 ± 1000 nm2 for the ALG layers). The optical dispersion functions of PDA, silicon dioxide and silicon were taken from previous reports [34][62]. The optical dispersion functions of ethanol, isobutanol, toluene and titanium dioxide were taken from the EP4-SE database. Contact

Low cost, p-ZnO/n-Si, rectifying, nano heterojunction diode: Fabrication and electrical characterization

• Vinay Kabra,
• Lubna Aamir and
• M. M. Malik

Beilstein J. Nanotechnol. 2014, 5, 2216–2221, doi:10.3762/bjnano.5.230

• Figure 1 shows the X-ray diffraction pattern of p-ZnO nanoparticles. The diffraction peaks of the sample correspond to the (100), (002), (101), (110), (103), and (112) planes of reflection for the hexagonal wurtzite structure of ZnO. All of the peaks are in good agreement with the JCPDS database file

Real-time monitoring of calcium carbonate and cationic peptide deposition on carboxylate-SAM using a microfluidic SAW biosensor

• Anna Pohl and
• Ingrid M. Weiss

Beilstein J. Nanotechnol. 2014, 5, 1823–1835, doi:10.3762/bjnano.5.193

• detail with the particular aim to inspire similar investigations in biomineralization research in the future. A standard database of the function of organic molecules, peptides and proteins in mineralizing systems will be a major achievement of global significance for materials science, biomedical

Quasi-1D physics in metal-organic frameworks: MIL-47(V) from first principles

• Danny E. P. Vanpoucke,
• Jan W. Jaeken,
• Stijn De Baerdemacker,
• Kurt Lejaeghere and
• Veronique Van Speybroeck

Beilstein J. Nanotechnol. 2014, 5, 1738–1748, doi:10.3762/bjnano.5.184

• the value for the majority spin component. Supporting Information Supporting information contains the spin-dependent optimized MIL-47(V) structures. These structures have also been deposited in the Cambridge Crystalographic Data Center database CCDC 1021380–1021384. Supporting Information File 148

Hydrophobic interaction governs unspecific adhesion of staphylococci: a single cell force spectroscopy study

• Nicolas Thewes,
• Peter Loskill,
• Philipp Jung,
• Henrik Peisker,
• Markus Bischoff,
• Mathias Herrmann and
• Karin Jacobs

Beilstein J. Nanotechnol. 2014, 5, 1501–1512, doi:10.3762/bjnano.5.163

• genome sequence of S. carnosus strain TM300 (deposited in the EMBL nucleotide database under accession number AM295250), 19 putative cell-wall anchored proteins harboring LPXTG motifs are predicted, including homologues of well-studied S. aureus adhesins such as clumping factor A and B, fibronectin

Protein-coated pH-responsive gold nanoparticles: Microwave-assisted synthesis and surface charge-dependent anticancer activity

• Dickson Joseph,
• Nisha Tyagi,
• Christian Geckeler and
• Kurt E.Geckeler

Beilstein J. Nanotechnol. 2014, 5, 1452–1462, doi:10.3762/bjnano.5.158

• P13006 for HST, LYS, OVA, BHG, BSA, TRY, and GOX, respectively) were downloaded from the UniProt protein database archive to calculate the compositions of the amino acid residues in the proteins. Synthesis of protein-coated AuNPs In a typical reaction, 5 mL of an aqueous solution containing 1 mg/mL of

Direct nanoscale observations of the coupled dissolution of calcite and dolomite and the precipitation of gypsum

• Francesco G. Offeddu,
• Jordi Cama,
• Josep M. Soler and
• Christine V. Putnis

Beilstein J. Nanotechnol. 2014, 5, 1245–1253, doi:10.3762/bjnano.5.138

• . The saturation index (SI) with respect to gypsum and calcite of the input solutions was calculated by using the PhreeqC code and the PhreeqC database [39]. The experimental strategy consisted of three stages. First, prior to each in-situ experiment an in-air image of a selected region of the cleaved

Organic and inorganic–organic thin film structures by molecular layer deposition: A review

• Pia Sundberg and
• Maarit Karppinen

Beilstein J. Nanotechnol. 2014, 5, 1104–1136, doi:10.3762/bjnano.5.123

Molecular biology approaches in bioadhesion research

• Marcelo Rodrigues,
• Birgit Lengerer,
• Thomas Ostermann and
• Peter Ladurner

Beilstein J. Nanotechnol. 2014, 5, 983–993, doi:10.3762/bjnano.5.112

• differential RNA-seq experiment can be compared to the established transcriptome database. 3. Spatial gene expression 3.1 Aim of in situ hybridization For detecting the spatial (and temporal) expression of genes within a tissue, ISH is a widespread and straightforward method. The principle of ISH can be used

Cytotoxic and proinflammatory effects of PVP-coated silver nanoparticles after intratracheal instillation in rats

• Nadine Haberl,
• Stephanie Hirn,
• Alexander Wenk,
• Jörg Diendorf,
• Matthias Epple,
• Blair D. Johnston,
• Fritz Krombach,
• Wolfgang G. Kreyling and
• Carsten Schleh

Beilstein J. Nanotechnol. 2013, 4, 933–940, doi:10.3762/bjnano.4.105

• after the instillation of 250 µg PVP-AgNP (Figure 8). Discussion According to the Woodrow–Wilson-Center database of nanotechnology-based products [28], silver is one of the most frequently used nanomaterials for consumer products. Due to the use of AgNP as aerosols in healthcare and hygiene spray

Simulation of electron transport during electron-beam-induced deposition of nanostructures

• Francesc Salvat-Pujol,
• Harald O. Jeschke and
• Roser Valentí

Beilstein J. Nanotechnol. 2013, 4, 781–792, doi:10.3762/bjnano.4.89

• one order of magnitude smaller than at 500 eV (cross section data taken from the numerical database of PENELOPE [7]). The photon spectrum was also examined with a deposit on top of the substrate. But no significant deviations regarding the minor role played by photon transport, as demonstrated for the

Synthesis of indium oxi-sulfide films by atomic layer deposition: The essential role of plasma enhancement

• Cathy Bugot,
• Nathanaëlle Schneider,
• Daniel Lincot and
• Frédérique Donsanti

Beilstein J. Nanotechnol. 2013, 4, 750–757, doi:10.3762/bjnano.4.85

• growth rate while using H2O as oxygen precursor and (b) GIXRD diffractogram. The reference diffraction pattern for In2S3 is taken from the database JCPDS 00-005-0731. Influence of the ratio of In2O3 cycles on the film absorption spectra when using H2O as oxygen precursor. Influence of a) the number of

Preparation of electrochemically active silicon nanotubes in highly ordered arrays

• Tobias Grünzel,
• Young Joo Lee,
• Karsten Kuepper and
• Julien Bachmann

Beilstein J. Nanotechnol. 2013, 4, 655–664, doi:10.3762/bjnano.4.73

• with an instrument model EL X-02 P Spec from DRE Dr. Riss Ellipsometerbau GmbH from 400 to 1000 nm. Fits were performed by using the database of material files provided with the instrument. Mixed layers were treated with the Lorentz–Lorentz model as implemented in the software of the instrument

Nano-structuring, surface and bulk modification with a focused helium ion beam

• Daniel Fox,
• Yanhui Chen,
• Colm C. Faulkner and
• Hongzhou Zhang

Beilstein J. Nanotechnol. 2012, 3, 579–585, doi:10.3762/bjnano.3.67

• in the spectra at ≈99 eV was observed to degrade from the top spectrum to the bottom. We compared our data to the spectra for crystalline and amorphous silicon from an online database [27]. The intensity of the peak at ≈99 eV is used as an indication of the crystallinity of the silicon. A higher