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BN++ – A Biological Information System

Jan Küntzer, Torsten Blum, Andreas Gerasch, Christina Backes, Andreas Hildebrandt, Michael Kaufmann, Oliver Kohlbacher, Hans-Peter Lenhof
2006 Journal of Integrative Bioinformatics  
BN++ is based on a comprehensive and extensible object model (BioCore), which has been implemented as a C++ framework, a Java class library, and a relational database.  ...  We illustrate the usefulness of BN++ with a few select example applications.Availability: BN++ is open source software available from our website at www.bnplusplus.org.  ...  Acknowledgements The authors would like to thank Thomas Schäfer and Marite Sirava for their work on the BN++ project. We are further grateful to Dr.  ... 
doi:10.1515/jib-2006-34 fatcat:cyefsqltzbh7bgghndsq77gkze

BN and BN oxide nanosheets based nanosensor for paracetamol adsorption: a first principles simulation

Miguel Castro, Ernesto Chigo Anota
2014 Mexican Journal of Materials Science and Engineering  
The paracetamol molecule promotes also a decrease of the reactivity parameter, which is crucial for biological applications of these systems.  ...  That is, these functionalized 2D systems yields appropriate conditions for field emission and they may be used as sensors of such pharmaceutical compound.  ...  biological applications.  ... 
doaj:376a921c11a143578eb3d337398e960c fatcat:tdg6mfp5ezaxrg3q5qjdk5b6oa

Electrophilic Aromatic Substitution of a BN Indole

Eric R. Abbey, Lev N. Zakharov, Shih-Yuan Liu
2010 Journal of the American Chemical Society  
We report the first examples of a "BN-fused" indole, and we demonstrate that this new family of unnatural indole derivatives undergoes electrophilic aromatic substitution (EAS) reactions with the same  ...  X-Ray structural analysis between BN indole and classic indole highlights significant differences in bond distances, in particular for bonds associated with the boron atom. NIH Public Access  ...  The bicyclic N-t-Bu-BN-indole 2 consists of a 6-membered 1,2-dihydro-1,2-azaborine heterocycle 14,15 and a lsy@uorgon.edu. Supporting Information Available.  ... 
doi:10.1021/ja107312u pmid:21043508 pmcid:PMC2990470 fatcat:ruljl24jyjhd5er7gw7lkjo3ui

Abstract analysis of pathways using the BN++ software framework

Jan Küntzer, Benny Kneissl, Oliver Kohlbacher, Hans-Peter Lenhof
2007 BMC Systems Biology  
analysis of pathways using the BN++ software framework  ...  With BN++, especially its C++ framework, we presented such a system [2] . In contrast to databases (e.g.  ...  However, the sheer amount and heterogeneity of the data pose a major challenge and call for an integrative system, allowing to manage all this information.  ... 
doi:10.1186/1752-0509-1-s1-p24 fatcat:aymxqsb43fdg7fs2mqv6qwypee

Suppression of 1/f Noise in Near-Ballistic h-BN-Graphene-h-BN Heterostructure Field-Effect Transistors [article]

Maxim A. Stolyarov, Guanxiong Liu, Sergey L. Rumyantsev, Michael Shur, Alexander A. Balandin
2015 arXiv   pre-print
The device channel was implemented with a single layer graphene encased between two layers of hexagonal boron nitride.  ...  We have investigated low-frequency 1/f noise in the boron nitride - grapheme - boron nitride heterostructure field - effect transistors on Si/SiO2 substrates (f is a frequency).  ...  A more informative characteristic of 1/f noise level in two-dimensional (2D) materials is the noise spectral density normalized to the device channel area, which we 3 | P a g e denote as parameter =(S  ... 
arXiv:1506.04083v1 fatcat:yxus4lj5pvf6jbnizm5eluqiwq

Suppression of 1/f noise in near-ballistic h-BN-graphene-h-BN heterostructure field-effect transistors

Maxim A. Stolyarov, Guanxiong Liu, Sergey L. Rumyantsev, Michael Shur, Alexander A. Balandin
2015 Applied Physics Letters  
Figure 4(a) shows the noise amplitude in our h-BN-G-h-BN HFET as a function of V GS -V D (V D is the Dirac voltage).  ...  Second, the stamp with PPC was brought into contact with the h-BN layer on a substrate using a micromanipulator.  ... 
doi:10.1063/1.4926872 fatcat:gmkydveyera3rh2jsvwpqgwoma

Use of a geographic information system to explore spatial variation in pathogen virulence and the implications for biological control of locusts and grasshoppers

Justine I. Klass, Simon Blanford, Matthew B. Thomas
2007 Agricultural and Forest Entomology  
The aim of the present study is to enhance the utility of this model by linking it with meteorological station data in a geographic information system (GIS) framework to investigate the spatial variation  ...  1 In a previous study, we developed a model to predict the effects of temperature on performance of a fungus-based biopesticide for controlling locusts and grasshoppers.  ...  Special thanks is extended to A.  ... 
doi:10.1111/j.1461-9563.2007.00336.x fatcat:y2bh7k2h7jam7fsjnugex5lxfe

BN+1 Bayesian network expansion for identifying molecular pathway elements

Andrew P. Hodges, Peter Woolf, Yongqun He
2010 Communicative & Integrative Biology  
Biological interaction networks and pathways have been simulated and analyzed by various computational methods, for example, Bayesian networks, 1,2 mutual information, 3,4 neural network, 5,6 and centrality  ...  A Bayesian network (BN) is a representation of a joint probability distribution over a set of random variables. 1 A BN includes two components: a directed acyclic graph (DAG) with vertices representing  ...  It would also be ideal to incorporate experimental descriptions and curated information when identifying the biological bases for the underlying interactions inferred by the BN+1 algorithm.  ... 
doi:10.4161/cib.3.6.12845 pmid:21331236 pmcid:PMC3038060 fatcat:kubkjzmvszcyba27ghyomnhf2y

UV-Photoelectron Spectroscopy of BN Indoles: Experimental and Computational Electronic Structure Analysis

Anna Chrostowska, Senmiao Xu, Audrey Mazière, Katherine Boknevitz, Bo Li, Eric R. Abbey, Alain Dargelos, Alain Graciaa, Shih-Yuan Liu
2014 Journal of the American Chemical Society  
Nucleus-independent chemical shifts calculations show that the introduction of boron into an aromatic 6π-electron system leads to a reduction in aromaticity, presumably due to a stronger bond localization  ...  Thus, electronic structure consequences resulting from BN/CC isosterism will need to be evaluated individually from system to system.  ...  Soc. 2014, 136, 11813−11820 ■ AUTHOR INFORMATION  ... 
doi:10.1021/ja5063899 pmid:25089659 pmcid:PMC4140474 fatcat:geooirid2bftfo4fz4voqn74cm

Purification and Characterization of the tRNA-processing Enzyme RNase BN

C. Callahan, D. Neri-Cortes, M. P. Deutscher
2000 Journal of Biological Chemistry  
RNase BN displays a number of unusual catalytic properties compared with the other exoribonucleases of E. coli.  ...  RNase BN, a tRNA-processing enzyme previously shown to be required for the 3-maturation of certain bacteriophage T4-encoded tRNAs, was overexpressed and purified to near homogeneity from Escherichia coli  ...  expression system (with changing of the medium to remove ␤-lactamase and to restore ampicillin levels) resulted in a 25-fold overproduction of RNase BN during the 4-h induction period.  ... 
doi:10.1074/jbc.275.2.1030 pmid:10625642 fatcat:3n3juv7kjjcffhqfcgasecwfba

Thermodynamically Controlled, Dynamic Binding of Diols to a 1,2-BN Cyclohexane Derivative

Gregory P. Harlow, Lev N. Zakharov, Gang Wu, Shih-Yuan Liu
2013 Organometallics  
The reversible covalent binding of diols to an N-Bn 1,2-BN cyclohexane has been studied by 11B and 1H NMR spectroscopy and single-crystal X-ray diffraction analysis.  ...  Deuterium labeling experiments demonstrate that ligand exchange is reversible and rapid at room temperature, and competitive binding studies establish diol association as a thermodynamically controlled  ...  The K eq data for systems 8−10 show that preorganization of the ligand into a cis geometry can improve the binding strength.  ... 
doi:10.1021/om400697r pmid:25798022 pmcid:PMC4364440 fatcat:zmuu3rpxwfddvi5fv52tkpniaa

p-SCN-Bn-HOPO: A Superior Bifunctional Chelator for 89Zr ImmunoPET

Melissa A. Deri, Shashikanth Ponnala, Paul Kozlowski, Benjamin P. Burton-Pye, Huseyin T. Cicek, Chunhua Hu, Jason S. Lewis, Lynn C. Francesconi
2015 Bioconjugate chemistry  
We successfully synthesized p-SCN-Bn-HOPO, a bifunctional derivative of 3,4,3-(LI-1,2-HOPO) as a potential chelator for 89 Zr.  ...  Recently, there has been a surge of interest in the development of an alternative chelator for 89 Zr 4+ to replace DFO, with several novel ligand systems being reported within the past year or so (Figure  ...  a difference in biological applications.  ... 
doi:10.1021/acs.bioconjchem.5b00572 pmid:26550847 pmcid:PMC4962612 fatcat:prfuk5wdtvf6ja6hc3d67jq4fm

NeuroSuites-BNs: An open web framework for massive Bayesian networks focused on neuroscience [article]

Mario Michiels, Pedro Larrañaga, Concha Bielza
2020 bioRxiv   pre-print
We present the capabilities of our proposed framework by highlighting a real example of a BN learned from genomic data obtained from Allen Institute for Brain Science.  ...  NeuroSuites-BNs is the first web framework for learning, visualizing, and interpreting Bayesian networks (BNs) that can scale to tens of thousands of nodes while providing fast and friendly user experience  ...  , and Fernando Rodriguez-820 Sanchez for his research in BN-based probabilistic clustering models and his help in reviewing that section in this paper.  ... 
doi:10.1101/2020.02.04.934174 fatcat:kt2jyyurdjcclogaohiv4hdeya

Scientific Opinion on the re-evaluation of Brilliant Black BN (E 151) as a food additive

2010 EFSA Journal  
In a recent study, Brilliant Black BN was found positive in a micronucleus test and a Comet assay in vitro.  ...  The Panel on Food Additives and Nutrient Sources added to Food provides a scientific opinion re-evaluating the safety of Brilliant Black BN (E 151).  ...  Information on existing authorisations and evaluations Brilliant Black BN is permitted as a food additive in the EU under Directive 94/36/EC.  ... 
doi:10.2903/j.efsa.2010.1540 fatcat:psettv4og5cq7bgbcs2nahckym

Rhodium-Catalyzed B–H Activation of 1,2-Azaborines: Synthesis and Characterization of BN Isosteres of Stilbenes

Alec N. Brown, Lev N. Zakharov, Tanya Mikulas, David A. Dixon, Shih-Yuan Liu
2014 Organic Letters  
Ten 1,2azaborine-based BN isosteres of stilbenes have been synthesized using this method, including a BN isostere of a biologically active stilbene.  ...  It is demonstrated that BN/CC isosterism in the context of stilbenes can lead to significant changes in the observed photophysical properties such as higher quantum yield and a larger Stokes shift.  ...  Ten examples of BN stilbenes have been synthesized using this method, including a BN isostere of a biologically active stilbene.  ... 
doi:10.1021/ol501362w pmid:24916200 pmcid:PMC4068778 fatcat:fv4yewxjj5g47b5c22gje2ffri
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