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

• ; cancer research; databases; nanomaterials; nanomedicine; Introduction The U.S. annual report to the nation on the state of cancer indicates a steady decline in overall mortality rates, with increases in incidence for many cancers [1]. Internationally, cancer incidence paints a more dramatic picture in

• ]. Databases such as dbGaP have provided investigators access to hundreds of genomics studies, resulting in three times that number of publications and scientific advances in the genetic basis of disease [8]. Unlike genomics, nanotechnology data management systems, which are at relatively early stages of

• address the needs of different communities. The task of creating relevant databases for nanotechnology risk assessment, manufacturing, characterizations, and literature data is being taken on globally by government, academic, and regulatory organizations. To date, there are approximately 38 databases at

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

• NPs drive toxicity. This work has shown that large databases of similar NPs with varying surface features studied under identical experimental design protocols, are invaluable in the development of models of nanoparticle-biological interactions. We have shown that intrinsic features of NPs

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

• 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

• separates NLP applications from other data processing systems is their use of knowledge about human language [12]. Many of the NLP applications utilize literature retrieved from databases. Information retrieval, document classification, and pattern matching methods are often utilized to ensure that the

• , and environmental risk assessment. Methods This review was limited to the English language literature included in two databases, PubMED and Web of Science [22][23]. The searches were conducted on February 12, 2015. For the search term (nano* AND “natural language processing”), Web of Science retrieved

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

• region(s) of interest (see section, Databases). The mass balance equations (Supporting Information File 1, Equations S1–S4) are then solved to determine the average ENM release rates to the environmental compartments (i.e., air, water, and soil). Mass “flows” of ENMs among the various compartments can be

• distribution (lower subplot). It is noted that such information can be utilized to convert MendNano reported ENM mass concentrations to surface area concentration [35][36] given the knowledge of the primary particle size. Databases The parameter database contains material properties, geographical, and

• ), compiled from various published studies [17], public databases [40], and market research [5], and estimated based on economic indicators [41]). Use cases for assessing multimedia distribution of ENMs The integrated RedNano simulation tool is suitable for a variety of assessments regarding the environmental

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

• facility 2.1 BLAST – basic local alignment search tool Basic local alignment search tool (BLAST) is a software package to query sequence databases for homologues [31]. Statistical information helps to determine the significance of every alignment. BLAST is widely used to analyze sequencing data and to find