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A Survey of Automatic Protocol Reverse Engineering Approaches, Methods, and Tools on the Inputs and Outputs View

Baraka D. Sija, Young-Hoon Goo, Kyu-Seok Shim, Huru Hasanova, Myung-Sup Kim
2018 Security and Communication Networks  
Additionally, we present discussion and extended classification in terms of automated to manual approaches, known and novel categories of reverse engineered protocols, and a literature of reverse engineered  ...  protocols in relation to the seven layers' OSI (Open Systems Interconnection) model.  ...  ProPrint [41] is a network trace based protocol fingerprint inference approach that focuses on distinguishing individual application protocols.  ... 
doi:10.1155/2018/8370341 fatcat:4zisozx6zjcu3fbgwwzncvn4b4

Improved Strategy for Comparing Microbial Assemblage Fingerprints

Ian Hewson, Jed A. Fuhrman
2006 Microbial Ecology  
The comparison of fingerprints relies upon the precise estimation of all amplified DNA fragment lengths, which correspond to operational taxonomic units (OTU; analogous, but not equal to, a taxon in macroorganism  ...  To account for OTU size calling imprecision, all fragments within a range of sizes (a window) can be combined (i.e., "binned") where the window is as wide as the imprecision of OTU size calling.  ...  A third approach, similar to the second, compares the relative amount of amplified DNA associated with each OTU, but calculates the parametric or nonparametric correlation coefficients (i.e., Pearson's  ... 
doi:10.1007/s00248-005-0144-9 pmid:16437287 fatcat:ikhdy4pygjavlbpqlhvnvzt4tm

Manipulation of Subcortical and Deep Cortical Activity in the Primate Brain Using Transcranial Focused Ultrasound Stimulation

Davide Folloni, Lennart Verhagen, Rogier B. Mars, Elsa Fouragnan, Charlotte Constans, Jean-François Aubry, Matthew F.S. Rushworth, Jérôme Sallet
2019 Neuron  
Here, we demonstrate that a focused transcranial ultrasound stimulation (TUS) protocol impacts activity even in deep brain areas: a subcortical brain structure, the amygdala (experiment 1), and a deep  ...  In control conditions without sonication, activity in a given area is related to activity in interconnected regions, but such relationships are reduced after sonication, specifically for the targeted areas  ...  DECLARATION OF INTERESTS The authors declare no competing interests.  ... 
doi:10.1016/j.neuron.2019.01.019 pmid:30765166 pmcid:PMC6520498 fatcat:bwtfnl7qj5hqfadnmgfliiyicu

Ecological inference on bacterial succession using curve-based community fingerprint data analysis, demonstrated with rhizoremediation experiment

Anu Mikkonen, Kaisa Lappi, Kaisa Wallenius, Kristina Lindström, Leena Suominen
2011 FEMS Microbiology Ecology  
A novel method to extract relative abundance data from the fingerprint curves for Shannon diversity index revealed contamination to reversibly decrease community complexity.  ...  To avoid the time-consuming and potentially subjective procedures of peak-based examination, we assessed the possibility to apply direct curve-based data analysis on community fingerprints produced with  ...  Acknowledgements We thank Marja Tiirola for advice in setting up the LH-PCR analysis and for the template DNA for LH-PCR standards, Leena A.  ... 
doi:10.1111/j.1574-6941.2011.01187.x pmid:22066474 fatcat:57vt6a6ynvetxnd526xfwfncmy

Quantitative Community Fingerprinting Methods for Estimating the Abundance of Operational Taxonomic Units in Natural Microbial Communities

A. Ramette
2009 Applied and Environmental Microbiology  
The approach was illustrated by using a quantitative version of automated ribosomal intergenic spacer analysis (ARISA), here called qARISA.  ...  A quantitative fingerprinting approach designated "qfingerprinting" is proposed here.  ...  ACKNOWLEDGMENTS I thank Susanne Menger for excellent technical assistance, Jed A. Fuhrman for helpful discussions about ARISA and binning, and Antje Boetius for critically reviewing the manuscript.  ... 
doi:10.1128/aem.02409-08 pmid:19201961 pmcid:PMC2675222 fatcat:qd66zcfwsrcidi5ds5mzm42hme

Identification of N2-fixing plant- and fungus-associated Azoarcus species by PCR-based genomic fingerprints

T Hurek, B Wagner, B Reinhold-Hurek
1997 Applied and Environmental Microbiology  
To facilitate species identification and strain comparison, we developed a protocol for PCR-generated genomic fingerprints, using an automated sequencer for fragment analysis.  ...  In contrast, the BOX-PCR assay (targeted to repetitive intergenic sequence elements of Streptococcus) yielded species-specific genomic fingerprints with some strain-specific differences.  ...  This work was supported by a grant from the Deutsche Forschungsgemeinschaft (Re756/5-1) to B.R.-H.  ... 
doi:10.1128/aem.63.11.4331-4339.1997 fatcat:wvwpoucc5nc2filziih7rybiyy

Identification of N2-fixing plant- and fungus-associated Azoarcus species by PCR-based genomic fingerprints

T Hurek, B Wagner, B Reinhold-Hurek
1997 Applied and Environmental Microbiology  
To facilitate species identification and strain comparison, we developed a protocol for PCR-generated genomic fingerprints, using an automated sequencer for fragment analysis.  ...  In contrast, the BOX-PCR assay (targeted to repetitive intergenic sequence elements of Streptococcus) yielded species-specific genomic fingerprints with some strain-specific differences.  ...  This work was supported by a grant from the Deutsche Forschungsgemeinschaft (Re756/5-1) to B.R.-H.  ... 
pmid:9361420 pmcid:PMC168753 fatcat:ciytgzh7izcpdafcpwzkc6trsm

Inferring Protocol State Machine from Network Traces: A Probabilistic Approach [chapter]

Yipeng Wang, Zhibin Zhang, Danfeng Yao, Buyun Qu, Li Guo
2011 Lecture Notes in Computer Science  
In our experiments, we evaluate a text-based protocol and two binary-based protocols to test the performance of Veritas.  ...  Our results show that the protocol state machines that Veritas infers can accurately represent 92% of the protocol flows on average.  ...  The essence of K-S test is to estimate the similarity of two samples according to their empirical probability distributions in a nonparametric way.  ... 
doi:10.1007/978-3-642-21554-4_1 fatcat:vi7wthplofhsdazd2edmh56lwa

A machine learning approach to TCP state monitoring from passive measurements

Desta Haileselassie Hagos, Paal E. Engelstad, Anis Yazidi, Oivind Kure
2018 2018 Wireless Days (WD)  
We would like to thank the Research Infrastructure Services Group at the University of Oslo for the use of multicore cluster machines.  ...  We would like to thank the Research Infrastructure Services Group at the University of Oslo for the use of multicore cluster machines. Acknowledgements.  ...  In Paper VI, we applied data-driven classification techniques based on probabilistic models and Bayesian inference by employing a novel non-stationary time series approach from a stochastic nonparametric  ... 
doi:10.1109/wd.2018.8361713 dblp:conf/wd/HagosEYK18 fatcat:hmeh7nfa7bbwxnncel5xnyytim

Gaussian processes online observation classification for RSSI-based low-cost indoor positioning systems

Maani Ghaffari Jadidi, Mitesh Patel, Jaime Valls Miro
2017 2017 IEEE International Conference on Robotics and Automation (ICRA)  
The proposed approach can perform online, does not rely on a particular sensor model or parameters, and is robust to sensor failures.  ...  However due to multipathing and shadowing effects, finding a unique sensor model using both parametric and nonparametric methods is highly challenging.  ...  The authors would also like to thank FX Palo Alto Laboratories Inc., for sharing Bluetooth Low Energy dataset collected by them to validate our proposed algorithm.  ... 
doi:10.1109/icra.2017.7989743 dblp:conf/icra/JadidiPM17 fatcat:opawlmv7hnhpfndwpaf2tib6n4

Behavioral Service Graphs: A formal data-driven approach for prompt investigation of enterprise and internet-wide infections

Elias Bou-Harb, Mark Scanlon
2017 Digital Investigation. The International Journal of Digital Forensics and Incident Response  
We evaluate the proposed approach in two deployment scenarios, namely, as an enterprise edge engine and as a global capability in a security operations center model.  ...  Publisher's version (a b s t r a c t The task of generating network-based evidence to support network forensic investigation is becoming increasingly prominent.  ...  To distinguish between sequential and permutation probing, we leverage the Mann-Kendall statistic test, a nonparametric hypothesis testing approach, to check for monotonicity in those distributions.  ... 
doi:10.1016/j.diin.2017.02.002 fatcat:lui3baw66jcknhmzseevdxrzc4

The next meta-challenge for Bioinformatics

Willy Valdivia-Granda
2008 Bioinformation  
Here, I briefly highlight some of the emerging challenges this new discipline presents to the computational biology community and point some of the opportunities to develop applications that can translate  ...  The direct sequencing of uncultivable organisms present in complex biological and environmental samples has opportunities to discover new life forms and metabolic processes.  ...  Acknowledgement: The author would like to thank Dr. Mya Breitbart and Francis Larson for the insightful comments and suggestions.  ... 
doi:10.6026/97320630002358 pmid:18685725 pmcid:PMC2478737 fatcat:vcivjjwhcjf3leqgy4sw4qov7m

A population genetic study of the endangered plant speciesLimonium dufourii(Plumbaginaceae) based on amplified fragment length polymorphism (AFLP)

CARMEN Palacios, STEPHEN Kresovich, FERNANDO González-Candelas
1999 Molecular Ecology  
DNA was extracted following a modified CTAB protocol described in Doyle (1991) .  ...  Modifications to the original protocol were as follows: a modified core mix was employed for the PSA and SA reactions which consisted of 1.5 mM MgCl 2 , 0.2 mM of each dNTP, 1× PCR Buffer II (PE), and  ...  Palacios to fulfil the requirements to obtain a PhD in Molecular and Evolutionary Genetics at the University of Valencia, under the supervision of Dr Gonz ‡lez-Candelas.  ... 
doi:10.1046/j.1365-294x.1999.t01-1-00597.x fatcat:uldquh2rtnhvvj4g7a5rcz4ofu

Outlier-Detection-Based Indoor Localization System for Wireless Sensor Networks

Yu-Chi Chen, Jyh-Ching Juang
2012 International Journal of Navigation and Observation  
The effectiveness of the proposed approach is verified experimentally in an indoor environment.  ...  The cheap and widely available measurement technique—received signal strength (RSS)—is usually taken into account in the indoor localization system, but the RSS measurements are known to be sensitive to  ...  Acknowledgment This work was sponsored by the National Science Council of Taiwan, under Grant NSC 98-2221-E-006-194-MY3.  ... 
doi:10.1155/2012/961785 fatcat:rh2ztf3oxjcf3myflefgfxva6u

Microeukaryotic diversity in the extreme environments of the Iberian Pyrite Belt: a comparison between universal and fungi-specific primer sets, temperature gradient gel electrophoresis and cloning

Mário Gadanho, José Paulo Sampaio
2006 FEMS Microbiology Ecology  
The fungi-specific primers contributed to a substantial increase in the number of fungal taxa found due, probably, to the relative low density of fungal structures.  ...  DNA was extracted from water samples and a set of eukaryotic universal primers directed to the small subunit rRNA genes (rDNA) was used.  ...  Acknowledgements The authors wish to thank Sandra Chaves and Rogério Tenreiro for assistance in cloning and TGGE experiments. M. Gadanho was supported by a grant SFRH/BD/1170/ 2000.  ... 
doi:10.1111/j.1574-6941.2006.00098.x pmid:16819957 fatcat:o6uykd3iurdk3num23o4fl2oce
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