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PuReD-MCL: a graph-based PubMed document clustering methodology

T. Theodosiou, N. Darzentas, L. Angelis, C. A. Ouzounis
2008 Bioinformatics  
Availability: Source code in perl and R are available from  ...  allows users to analyse the results by highlighting important clues, and finally to visualise the clusters and all relevant information using an interactive graph layout algorithm, for instance BioLayout Express  ...  ND is supported by an ENTER grant from the General Secretariat for Research and Technology of the Hellenic Ministry of Development.  ... 
doi:10.1093/bioinformatics/btn318 pmid:18593717 fatcat:lrzh4yxc7jebrdzpwwqkgws7hy

The Unconventionality of Nature: Biology, from Noise to Functional Randomness [chapter]

Barbara Bravi, Giuseppe Longo
2015 Lecture Notes in Computer Science  
In biology, phenotypes' variability stems from stochastic gene expression as well as from extrinsic fluctuations that are largely based on the contingency of developmental paths and on ecosystemic changes  ...  In contrast to physical conservation properties, thus symmetries, symmetry breaking is particularly relevant in biology; it provides another key component of biological historicity and of randomness as  ...  Acknowledgements We thank Angelo Vulpiani for stimulating remarks on a preliminary draft and Peter Sollich for a careful reading of part of the manuscript.  ... 
doi:10.1007/978-3-319-21819-9_1 fatcat:hsqpwn3avrguli3x5wbecogsk4

International Journal of Biology, Vol. 1, No. 1, January 2009

Editor IJB
2009 International Journal of Biology  
Rezia Khatun, Scientific Officer, BLRI is gratefully acknowledged for performing the feed analysis. Special thanks to Dr.  ...  I thank the reviewers for their contributions to improvement of the manuscript.  ...  Again closer analysis of the E.coli data needs to be undertaken which can be seen in Figure 4 .  ... 
doi:10.5539/ijb.v1n1p0 fatcat:rqmbs35dcvfn5eema3f2li7jmu

Abstracts 2019 Joint IOCV XXI and IRCHLB VI

Organization IOCV, Committee IRCHLB
2019 Journal of citrus pathology  
Abstracts 2019 Joint IOCV XXI and IRCHLB VI Permalink Journal Abstract: The availability of pathogen tested, true-to-type propagative material is critical for  ...  The technique of shoot-tip grafting in vitro (STG) was developed to recover citrus  ...  All the genes required for flagella and Type IV pili are present in CLas, but neither active motility nor flagella or pili have been reported for CLas.  ... 
doi:10.5070/c461045425 fatcat:2u4l5yqoifewxfp5zptqmfj3i4


2009 Antonie van Leeuwenhoek. International Journal of General and Molecular Microbiology  
Soon after the beginning of the outbreak in 2007, a multidisciplinary Qfever team developed a provisionally protocol 1 for diagnosis and treatment of acute and chronic Q fever 1 .  ...  A titer of [ = 1:64 was considered positive both for the IgG as for the IgM IFA. In the IgG ELISA, a value of [ = 20 IU/ml was positive.  ...  AC Schürch 1 , K Kremer 1 , O Daviena 1 , A Kiers 2 , MJ Boeree 3 , This project is financially supported by The Netherlands Ministry of Economic Affairs and the B-Basic partner organizations (  ... 
doi:10.1007/s10482-009-9328-5 pmid:19343545 fatcat:vliejbeyvvhgnasah7ei7khzhe


2018 Seibutsu Butsuri  
In this symposium, each speaker will make 10-minute presentation followed by 3-minute discussion as the second round of screening.  ...  Up to five awardees of the Early Career Award in Biophysics will be selected and announced at the banquet 3SEA-5 光遺伝子操作による単一の糸球体の活性により誘因される恐怖行動の探索 Immobility responses are induced by photoactivation of  ...  Our recent analysis of 17 cell lines of human iPS cells will also be introduced. 2O1412 Quantifying heterogeneity of stochastic gene expression Keita Iida 1 , Nobuaki Obata 2 , Yoshitaka Kimura 1 ( 1  ... 
doi:10.2142/biophys.58.s1 fatcat:6slkwnu64fen7cjixehxrcmdzm

The 28th Annual Symposium of The Protein Society: Program & Abstracts

2014 Protein Science  
Subsequent analysis revealed that the S287N variant conferred a high level of ceftazidime resistance on E.coli compared to wild-type AmpC.  ...  Human Immunodeficiency Virus type-1 (HIV-1) is a causative agent of AIDS.  ...  POST 07-391 Analysis of Several Monomeric Mutants of Triosephosphate Isomerase Misrain E. Gurrola Acosta 1 , Maria E.  ... 
doi:10.1002/pro.2504 pmid:25043257 pmcid:PMC4116645 fatcat:yjhug3aif5futn3icovvrkgebm

Thirty-seventh Annual Meeting February 14-18, 1993 Washington Convention Center Washington, D.C. Tuesday Symposia and Posters, Part IV

1993 Biophysical Journal  
Perneabilizd synaptosomes (.25mg/ml saponin) were incubated in an itracelular ionic media at pH 7.4 (20mM Heps), 370C, and 3mM ATP for either 1, 10, 30, or60 secondin the presence of four different EGTA  ...  pipette, and the cell clamped at -70 mV to prevent depolarization dependent Ca2+ entry, the rate of rise of C" after cell "pop-in" was enhanced by the presence of 150 AM cAMP in the pipette.  ...  USAThe rates of proton release and uptake in the R82A mutant of bacteriorhodopsin were measured in a) micelles of R82A (expressed in E.coli) with the pH-indicator fluorescein attached to G72C on the extracellular  ... 
doi:10.1016/s0006-3495(93)81407-3 fatcat:e2el5ck7qneidoaqcbrj4lmbs4


Settore Disciplinare, Ssd Bio
Acknowledgments I wish to thank Isabel Delany at GSK Vaccines in Siena, for her precious help and support during the PhD program.  ...  I would like to thank also Vincenzo Scarlato from University of Bologna for his support and his thoughtful feedbacks and discussion.  ...  For adhesion analysis, E.coli wild type or expressing NadA were added at a multiplicity of infection (MOI) of 100 and allowed to adhere for 3 h at 37°C and 5% CO2.  ... 

Resource Letter: Bio-molecular Nano-machines: where Physics, Chemistry, Biology and Technology meet [article]

Debashish Chowdhury
2008 arXiv   pre-print
Although, traditionally, these machines were subjects of investigation in biology and biochemistry, increasing use of the concepts and techniques of physics in recent years have contributed to the quantitative  ...  The possibility of exploiting these principles for the design and control of artificial nano-machines has opened up a new frontier in the bottom-up approach to nano-technology.  ...  Type I topoisomerases can change the linking number of a closed circular DNA in steps of ±1 whereas type II topoisomerases change the linking number in steps of ±2.  ... 
arXiv:0807.2731v1 fatcat:ho2pcrnn4ndp3haxuijbdtpo6y

In vitro Reconstitution of DegP-Omp complexes from Escherichia coli

Julia Leodolter
2010 unpublished
The bifunctionial heat-shock protein DegP, a member of the HtrA family, functions both as a protease and a chaperone and plays a key role in protein quality control in the E.coli periplasm.  ...  von E.coli inne.  ...  Acknowledgements Acknowledgements We thank for the generous help of K. Mechtler and I. Steinmacher for mass spectrometry, M. Madalinki for peptide synthesis and G.Resch for electron microscopy.  ... 
doi:10.25365/thesis.12782 fatcat:45y3kvudmfhcrpud7qmchw26ju

Mathematical Modelling of Bacteria and Phage: Coevolution, Ecology and Stochastic Decision Making

Matthew Robb, Vahid Shahrezaei, Ivana Gudelj, Natural Environment Research Council (Great Britain)
At the single cell level, stochastic modelling of genetic networks was used to develop a mechanistic understanding of decision making in lambda phage.  ...  Models developed in this thesis reveal the importance of connecting work at the single cell level and population scale level and also the significance of of global cell effects of noise in cellular systems  ...  In this work we assume that expression of mRNA and proteins are stochastic, in addition to cell partitioning.  ... 
doi:10.25560/23988 fatcat:h7gzx4pterby3m5c5z6n5xzjpu


Dove,S.L. et al. (1997) Control of Escherichia coli type 1 fimbrial gene expression in stationary phase: a negative role for RpoS. Mol. Gen. Genet. 254: 13-20.  ...  Type F pili are encoded by natural conjugative plasmids, which thus direct the expression of biofilm factors as a part of a coordinated strategy aimed to their propagation (Ghigo, 2001 ).  ...  coli strain expressing the wspR gene.  ... 
doi:10.13130/rossi-elio_phd2014-01-24 fatcat:ylmtt2htxrfpdhhgmg3wdpgusq


Conflict of interest None declared. References Acknowledgements 312 This work was supported by grants from the Lundbeck Foundation to MF, and the Danish Council  ...  Type F pili are encoded by natural conjugative plasmids, which thus direct the expression of biofilm factors as a part of a coordinated strategy aimed to their propagation (Ghigo, 2001) .  ...  There are different types of pili, with different composition and biosynthesis, depending on the bacterial species.  ... 
doi:10.13130/gambino-michela_phd2015-05-28 fatcat:eddlyesvrfbcpctwn4z3jhq65q

Spatial regulation of dual flagellar systems

Florian Roßmann, Thormann, Kai (Prof. Dr.)
Since the positions of both the polar and lateral flagella play key roles in this special movement pattern, the mode of action of the regulator [...]  ...  Examples of compartmentalized processes are those involved in bacterial motility.  ...  We acknowledge the assistance of the Acknowledgements This project was supported by grants from the Deutsche Forschungsgemeinschaft (DFG) to KMT (TH831/5-1) in the framework of the priority program  ... 
doi:10.17192/z2017.0061 fatcat:huqcnpml3jgmzmqc3i5zks4v7q
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