Application of biclustering of gene expression data and gene set enrichment analysis methods to identify potentially disease causing nanomaterials

• Andrew Williams and
• Sabina Halappanavar

Beilstein J. Nanotechnol. 2015, 6, 2438–2448, doi:10.3762/bjnano.6.252

• median. The median was used as it is a robust estimate of the central tendency. For each experimental condition, the data was further normalized by centering to the matched control. The control samples were then removed from the data set. The remaining data is presented relative to the control

Negative differential electrical resistance of a rotational organic nanomotor

• Hatef Sadeghi,
• Sara Sangtarash,
• Qusiy Al-Galiby,
• Rachel Sparks,
• Steven Bailey and
• Colin J. Lambert

Beilstein J. Nanotechnol. 2015, 6, 2332–2337, doi:10.3762/bjnano.6.240

• Hatef Sadeghi Sara Sangtarash Qusiy Al-Galiby Rachel Sparks Steven Bailey Colin J. Lambert Quantum Technology Centre, Department of Physics, Lancaster University, LA1 4YB Lancaster, UK 10.3762/bjnano.6.240 Abstract A robust, nanoelectromechanical switch is proposed based upon an asymmetric

Kelvin probe force microscopy for local characterisation of active nanoelectronic devices

• Tino Wagner,
• Hannes Beyer,
• Patrick Reissner,
• Philipp Mensch,
• Heike Riel,
• Bernd Gotsmann and
• Andreas Stemmer

Beilstein J. Nanotechnol. 2015, 6, 2193–2206, doi:10.3762/bjnano.6.225

• superior resolution of FM-KFM while maintaining robust topography feedback and minimal crosstalk, we introduce a novel FM-KFM controller based on a Kalman filter and direct demodulation of sidebands. We discuss the origin of sidebands in FM-KFM irrespective of the cantilever quality factor and how direct

• sideband demodulation enables robust amplitude modulated topography feedback. Finally, we demonstrate our single-scan FM-KFM technique on an active nanoelectronic device consisting of a 70 nm diameter InAs nanowire contacted by a pair of 120 nm thick electrodes. Keywords: capacitive crosstalk; frequency

Controlled switching of single-molecule junctions by mechanical motion of a phenyl ring

• Yuya Kitaguchi,
• Satoru Habuka,
• Hiroshi Okuyama,
• Shinichiro Hatta,
• Tetsuya Aruga,
• Thomas Frederiksen,
• Magnus Paulsson and
• Hiromu Ueba

Beilstein J. Nanotechnol. 2015, 6, 2088–2095, doi:10.3762/bjnano.6.213

• retraction were recorded. The height of the plateau, corresponding to the conductance for each molecule, is robust between repeated measurements and is larger by a factor of ≈2 for PhS. This demonstrates that the conductance is modified by chemical substitution of the anchoring atom from oxygen to sulfur. To

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

• in distinct datasets are related. Data integration within searchable databases supports computational modelling via enabling data from multiple sources to be combined, in principle, for more robust, generalisable analysis and via facilitating the identification of data which are relevant to the needs

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

• property of cytotoxicity, but also indicates that further studies including much larger data sets are necessary to develop reliable and robust classification methods that can be apply to a broader set of compounds, cell cultures and experimental designs. Conclusion In this study, classification methods for

Analysis of soil bacteria susceptibility to manufactured nanoparticles via data visualization

• Rong Liu,
• Yuan Ge,
• Patricia A. Holden and
• Yoram Cohen

Beilstein J. Nanotechnol. 2015, 6, 1635–1651, doi:10.3762/bjnano.6.166

• ], providing a dendrogram of hierarchical similarity among the treatments. In the hierarchical clustering, average-link (defined as for two clusters Ci and Cj) was used as inter-cluster distance measure since it is robust to outliers [38][39]. An advantage of the hierarchical clustering based on the L1

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

• between clusters might happen making determination of the cluster number the first concern. Although there are several algorithms to decide the cluster number, the lack of robust data sets such as this preclude a current understanding of which algorithm may be appropriate [48]. Kriging estimation Based on

Possibilities and limitations of advanced transmission electron microscopy for carbon-based nanomaterials

• Xiaoxing Ke,
• Carla Bittencourt and
• Gustaaf Van Tendeloo

Beilstein J. Nanotechnol. 2015, 6, 1541–1557, doi:10.3762/bjnano.6.158

• high resolution, manufacturers went on to higher operation voltages in the sixties and seventies of the twentieth century [2][3][4][5]. This came at the price of increasing beam damage, and consequently separated the study of hard matter (metal or robust inorganic materials) and soft matter

Continuum models of focused electron beam induced processing

• Milos Toth,
• Charlene Lobo,
• Vinzenz Friedli,
• Aleksandra Szkudlarek and
• Ivo Utke

Beilstein J. Nanotechnol. 2015, 6, 1518–1540, doi:10.3762/bjnano.6.157

• profile of such gas injection systems. The capillaries are useful because they simultaneously assure a high local molecule flux at the substrate surface, and a low vacuum chamber background pressure, as required for robust operation of the vacuum system. However, a disadvantage of a capillary-style GIS is

Current–voltage characteristics of manganite–titanite perovskite junctions

• Benedikt Ifland,
• Patrick Peretzki,
• Birte Kressdorf,
• Philipp Saring,
• Andreas Kelling,
• Michael Seibt and
• Christian Jooss

Beilstein J. Nanotechnol. 2015, 6, 1467–1484, doi:10.3762/bjnano.6.152

• using the convolution functions fSCR and fSCR+D, an integrated EBIC linescan, ΣIEBIC, can be described for both cases. By dividing these two factors, the integrated generation volume is canceled out and leaves only: which can be used as a robust estimate for Lp + Ln if the width of the SCR is known

Peptide-equipped tobacco mosaic virus templates for selective and controllable biomineral deposition

• Klara Altintoprak,
• Axel Seidenstücker,
• Alexander Welle,
• Sabine Eiben,
• Petia Atanasova,
• Nina Stitz,
• Alfred Plettl,
• Joachim Bill,
• Hartmut Gliemann,
• Holger Jeske,
• Dirk Rothenstein,
• Fania Geiger and
• Christina Wege

Beilstein J. Nanotechnol. 2015, 6, 1399–1412, doi:10.3762/bjnano.6.145

• regular-shaped, readily available nanorod biotemplates with inorganic compounds has attracted increasing interest during recent years. The goal is an effective, bioinspired fabrication of fiber-reinforced composites and robust, miniaturized technical devices. Major challenges in the synthesis of

Electrical characterization of single molecule and Langmuir–Blodgett monomolecular films of a pyridine-terminated oligo(phenylene-ethynylene) derivative

• Henrry M. Osorio,
• Santiago Martín,
• María Carmen López,
• Santiago Marqués-González,
• Simon J. Higgins,
• Richard J. Nichols,
• Paul J. Low and
• Pilar Cea

Beilstein J. Nanotechnol. 2015, 6, 1145–1157, doi:10.3762/bjnano.6.116

• containing two different groups, each capable of interacting with the substrate, cannot be prepared by this method [30]. Also, the molecule–substrate and molecule–molecule interactions required for the formation of robust, well-ordered SA films result in a rather limited number of metal–organic interfaces

• available to be studied [31][32]. Electrografted molecules form robust bonds with the underlying substrate but are typically not as well ordered as SA or LB films, and the growth of less defined multilayers is common with this method [33]. The LB technique requires a tedious fabrication process; however

Charge carrier mobility and electronic properties of Al(Op)₃: impact of excimer formation

• Andrea Magri,
• Pascal Friederich,
• Bernhard Schäfer,
• Valeria Fattori,
• Xiangnan Sun,
• Timo Strunk,
• Velimir Meded,
• Luis E. Hueso,
• Wolfgang Wenzel and
• Mario Ruben

Beilstein J. Nanotechnol. 2015, 6, 1107–1115, doi:10.3762/bjnano.6.112

• efficiently accept and delocalize additional electrons) suggest more robust electron charge transport properties. This discrepancy is explained by the excimer formation, whose inclusion in the multiscale simulation workflow is expected to bring the theoretical simulation and experiment into agreement

Automatic morphological characterization of nanobubbles with a novel image segmentation method and its application in the study of nanobubble coalescence

• Yuliang Wang,
• Huimin Wang,
• Shusheng Bi and
• Bin Guo

Beilstein J. Nanotechnol. 2015, 6, 952–963, doi:10.3762/bjnano.6.98

• method is robust to the selection of the threshold value during contour initialization. (a) Initialized contour obtained with a lower threshold value (10 nm) and corresponding converged contour obtained using the proposed method. (b) Initialized contour obtained with a higher threshold value (18 nm) and

• corresponding converged contour. (c) Comparison of the initialized contours and the converged contours obtained with the different threshold values. The coverged contours are superimposed on each other, which indicates that the proposed method is robust to the selection of the threhold value. Implementation of

Stiffness of sphere–plate contacts at MHz frequencies: dependence on normal load, oscillation amplitude, and ambient medium

• Jana Vlachová,
• Rebekka König and
• Diethelm Johannsmann

Beilstein J. Nanotechnol. 2015, 6, 845–856, doi:10.3762/bjnano.6.87

• both the linear and the nonlinear regime. All experiments were repeated 9 times, which allows for a robust analysis of statistical errors. Finally, we compare experiments undertaken in air to experiments using the same sample, but immersed in water. Experimental Modeling A QCM loaded with discreate

• readily extracted from the data by extrapolation (see Figure 5 and Figure 7 below). Likewise, the friction coefficient as derived from the slopes of Δf(u0) and ΔΓ(u0) is a robust parameter (see Figure 8 below). Very rarely, we see an increase of Δf with amplitude (data not shown). This behavior might

Microwave assisted synthesis and characterisation of a zinc oxide/tobacco mosaic virus hybrid material. An active hybrid semiconductor in a field-effect transistor device

• Shawn Sanctis,
• Rudolf C. Hoffmann,
• Sabine Eiben and
• Jörg J. Schneider

Beilstein J. Nanotechnol. 2015, 6, 785–791, doi:10.3762/bjnano.6.81

• Biology and Plant Virology, University of Stuttgart, 70550 Stuttgart, Germany 10.3762/bjnano.6.81 Abstract Tobacco mosaic virus (TMV) has been employed as a robust functional template for the fabrication of a TMV/zinc oxide field effect transistor (FET). A microwave based approach, under mild conditions

• and 2D biological molecules as structure-directing agents, enabling a "bottom-up" approach for building these complex nanoarchitectures. Among the several biological templates, the tobacco mosaic virus (TMV) has shown great potential to function as a robust biological template for the deposition of a

Production, detection, storage and release of spin currents

• Michele Cini

Beilstein J. Nanotechnol. 2015, 6, 736–743, doi:10.3762/bjnano.6.75

• current, excited by the spin–orbit interaction in the ring. This behavior is analytically described in [12] and is found to be robust with respect to temperature and small deviations from half filling. The main results of the present paper concern possible schemes to detect, store, gather, and then

Electroburning of few-layer graphene flakes, epitaxial graphene, and turbostratic graphene discs in air and under vacuum

• Andrea Candini,
• Nils Richter,
• Domenica Convertino,
• Camilla Coletti,
• Franck Balestro,
• Wolfgang Wernsdorfer,
• Mathias Kläui and
• Marco Affronte

Beilstein J. Nanotechnol. 2015, 6, 711–719, doi:10.3762/bjnano.6.72

• assure a high mechanical stability even above room temperature. Finally, the possibility to exploit specific functionalizations to attach the molecular units to the graphene electrodes through carbon bonds and/or π-stacking seems to be a promising route to develop well-defined and robust junction

• value of d is a quite robust fitting parameter, while the other two are not, since good fits are still possible even with very different values. Indeed, we can fit our data with almost the same accuracy by using a very broad range of values for A and Φ (see the Supporting Information File 1 for some

Mandibular gnathobases of marine planktonic copepods – feeding tools with complex micro- and nanoscale composite architectures

• Jan Michels and
• Stanislav N. Gorb

Beilstein J. Nanotechnol. 2015, 6, 674–685, doi:10.3762/bjnano.6.68

• sharp tooth-like structures (called ‘teeth’ in the following), and the number of teeth is smaller than those of the gnathobases of the other two groups (Figure 2b); (2) copepod species that mainly feed on phytoplankton possess robust gnathobases with compact and relatively short teeth at their distal

Entropy effects in the collective dynamic behavior of alkyl monolayers tethered to Si(111)

• Christian Godet

Beilstein J. Nanotechnol. 2015, 6, 583–594, doi:10.3762/bjnano.6.60

• ][33][34][35]. These robust densely packed insulating molecular layers play the role of nanometer-thick tunnel barriers [25][27][31][32][36][37][38][39]. Although conformational changes are intrinsic to soft matter, the consequences of temperature-induced [25][26][27][31] and pressure-induced [7][9

Pulmonary surfactant augments cytotoxicity of silica nanoparticles: Studies on an in vitro air–blood barrier model

• Jennifer Y. Kasper,
• Lisa Feiden,
• Maria I. Hermanns,
• Christoph Bantz,
• Michael Maskos,
• Ronald E. Unger and
• C. James Kirkpatrick

Beilstein J. Nanotechnol. 2015, 6, 517–528, doi:10.3762/bjnano.6.54

• depend on the chemical surface properties of the aSNPs. Reactive silanol groups seem to play a crucial role for an augmented toxicity of aSNPs. The A549 cells in the coculture seem to be more robust towards aSNPs, which might be a result of a higher differentiation and polarization state due the longer

• lung surfactant. In addition, a higher differentiation and polarization state of A549 as it occurs in the coculture resembles more closely the in vivo situation, as they seem to be more robust towards aSNPs with respect to their membrane integrity, but still sensitive regarding their inflammatory

Palladium nanoparticles anchored to anatase TiO₂ for enhanced surface plasmon resonance-stimulated, visible-light-driven photocatalytic activity

• Kah Hon Leong,
• Hong Ye Chu,
• Shaliza Ibrahim and
• Pichiah Saravanan

Beilstein J. Nanotechnol. 2015, 6, 428–437, doi:10.3762/bjnano.6.43

• Honda in 1972 [1]. To date, TiO2 is still the most favorable choice owing to its versatility and robust advantages that include photostability, non-toxicity, low cost, chemical and biological inertness, high photocatalytic activity and favorable optoelectronic properties [2][3][4][5]. TiO2 also

• -dimensional anatase TiO2/Ag, which exhibited an excellent photocatalytic activity with almost 100% degradation of 2,4-dichlorophenol within 2 h [26]. Likewise, Hou et al. reported a 9-fold improvement in the photocatalytic decomposition rate of methyl orange driven by a photocatalyst consisting of robust

A surface acoustic wave-driven micropump for particle uptake investigation under physiological flow conditions in very small volumes

• Florian G. Strobl,
• Dominik Breyer,
• Phillip Link,
• Adriano A. Torrano,
• Christoph Bräuchle,
• Matthias F. Schneider and
• Achim Wixforth

Beilstein J. Nanotechnol. 2015, 6, 414–419, doi:10.3762/bjnano.6.41

• -driven systems is their applicability to very small samples without having to deal with any dead volume. Thus, the demand for sample material is extremely low and the small surfaces in general reduce the risk of sample contamination. Moreover, the devices are typically very robust and inexpensive to

Dynamic force microscopy simulator (dForce): A tool for planning and understanding tapping and bimodal AFM experiments

• Horacio V. Guzman,
• Pablo D. Garcia and
• Ricardo Garcia

Beilstein J. Nanotechnol. 2015, 6, 369–379, doi:10.3762/bjnano.6.36

• simulate the full cantilever dynamics in both amplitude modulation and bimodal AM force microscopies. The code is both robust and numerically accurate. It incorporates the most relevant interaction force models that apply for dynamic AFM experiments in air and liquid. The simulator has been tested over the