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Fundamental identifiability limits in molecular epidemiology

Stilianos Louca, Angela McLaughlin, Ailene MacPherson, Jeffrey B Joy, Matthew W Pennell, Keith Crandall
2021 Molecular biology and evolution  
It remains generally unknown, however, how robust phylodynamic epidemiological inferences are, especially when there is uncertainty regarding pathogen prevalence and sampling intensity.  ...  from phylogenetic data alone; rather, estimators can only converge to the "congruence class" of the true dynamics.  ...  This project was supported by a GCRC grant from the University of British Columbia.  ... 
doi:10.1093/molbev/msab149 pmid:34009339 pmcid:PMC8382926 fatcat:j7g5q3lp4nhh7me7ga5gbwt76a


Ryan C. Garrick, David M. Rowell, Chris S. Simmons, David M. Hillis, Paul Sunnucks
2008 Evolution  
This general pattern of phylogeographic congruence was accompanied by evidence for contemporaneous demographic incongruence indicating that, even at relatively small spatial scales, biogeographic context  ...  Our data revealed a general pattern of broad-scale similarities in species' responses to the interaction between Pleistocene climatic cycles and landscape setting, overlaid with some species-specific differences  ...  Hillis, Bull and Cannatella laboratory members provided a valuable forum for discussion. P. Beerli and G. Jacquez generously gave advice on MIGRATE and boundary overlap analyses, respectively. C.  ... 
doi:10.1111/j.1558-5646.2008.00349.x pmid:18298648 fatcat:evfivsaptfg6fchfqwhj5ej7de

Inferring the Ancient History of the Translation Machinery and Genetic Code via Recapitulation of Ribosomal Subunit Assembly Orders

Gregory P. Fournier, Justin E. Neumann, J. Peter Gogarten, Joel S. Bader
2010 PLoS ONE  
Given this model, we produce a probabilistic evolutionary ordering of the universally conserved small subunit (SSU) and large subunit (LSU) ribosomal proteins.  ...  Optimizing the relative ordering of SSU and LSU evolutionary chronologies with respect to minimizing differences in amino acid usage bias, we find strong compositional evidence for a more ancient origin  ...  Subtracting a matrix of average RMSD values generated from randomized AA usage data (B) from raw RMSD scores (A), a matrix of residuals is generated (C), free of potential artifacts imposed by the model  ... 
doi:10.1371/journal.pone.0009437 pmid:20208990 pmcid:PMC2830423 fatcat:6xenujto7zefxlg7cvl26vs3ve

Page 3957 of Mathematical Reviews Vol. , Issue 91G [page]

1991 Mathematical Reviews  
sequences produced by pseudo-random number generators.  ...  Us- ing this general method, specific examples of generators having this form, the linear congruential method, linear congruences with n terms in the recurrence, and quadratic congruences are shown to  ... 

Abstract interpretation of microcontroller code: Intervals meet congruences

Jörg Brauer, Andy King, Stefan Kowalewski
2013 Science of Computer Programming  
To prove this and related properties, this article advocates using the domain of bit-wise linear congruences in conjunction with intervals to derive accurate range information.  ...  In particular, since registers are often memory mapped, it is necessary to show that an indirect store operation does not accidently mutate a register.  ...  Such a sequence can be found by considering the control flags: BRNE depends on Z hence we include CPC R31 R17 in the sequence since it effects Z.  ... 
doi:10.1016/j.scico.2012.06.001 fatcat:oeeof676pnaorpgq4snkb6bb3e

The performance of the Congruence Among Distance Matrices (CADM) test in phylogenetic analysis

Véronique Campbell, Pierre Legendre, François-Joseph Lapointe
2011 BMC Evolutionary Biology  
CADM is a statistical test used to estimate the level of Congruence Among Distance Matrices.  ...  It was applied to additive distance matrices representing phylogenies and to genetic distance matrices obtained from nucleotide sequences of different lengths that were simulated on randomly generated  ...  This study was supported by NSERC and FQRNT scholarships to VC and by NSERC grant OGP0155251 to FJL.  ... 
doi:10.1186/1471-2148-11-64 pmid:21388552 pmcid:PMC3065422 fatcat:74rtcmgu3nhljevkuhipdfu3q4

NEMESYS: Network Message Syntax Reverse Engineering by Analysis of the Intrinsic Structure of Individual Messages

Stephan Kleber, Henning Kopp, Frank Kargl
2018 Workshop on Offensive Technologies  
Thereby, message formats of unknown protocols can be inferred. We present a novel method to infer structure from network messages of binary protocols.  ...  Additionally, we introduce the Format Match Score: the first quantitative measure of the quality of a message format inference.  ...  Future Work NEMESYS generates message segments from the change in Bit Congruence between bytes.  ... 
dblp:conf/woot/KleberKK18 fatcat:gimzkmrdy5dg5hdnfhgzen6na4

On the existence of recurrent structures & statistical bias in the Collatz path sequences [article]

Sawon Pratiher, Subhasis Kundu
2017 arXiv   pre-print
This is followed by a closed form finite state machine (FSM) model of these recurrences using a set of linear congruence equations resulting in a different terminating condition for the Collatz problem  ...  Also if the presented analysis can be made rigorous to solve the set of linear congruence equations for the Collatz FSM model, the exact true nature of Collatz problem can be inferred.  ...  followed by a model formulation of these repetitive patterns by means of functional equations involving a set linear congruence equations.  ... 
arXiv:1608.03600v6 fatcat:6v3zfis5ancd7o7tnucztwtese

Fly Photoreceptors Encode Phase Congruency

Uwe Friederich, Stephen A. Billings, Roger C. Hardie, Mikko Juusola, Daniel Coca, Samuel G. Solomon
2016 PLoS ONE  
We demonstrate that to mitigate for the inherent sensitivity to noise of the local phase congruency measure, the nonlinear coding mechanisms of the fly photoreceptors are tuned to suppress random phase  ...  Drosophila photoreceptors and show for the first time that photoreceptors exploit nonlinear dynamics to selectively enhance and encode phase-related features of temporal stimuli, such as local phase congruency  ...  temporal stimulus sequence generated by scanning line-by-line the image on the left.  ... 
doi:10.1371/journal.pone.0157993 pmid:27336733 pmcid:PMC4919002 fatcat:trflybxlmbekxobbturr66lwsi

Phylogenetic congruence betweenMollitrichosiphum(Aphididae: Greenideinae) andBuchneraindicates insect-bacteria parallel evolution

2012 Systematic Entomology  
The congruence between the phylogenetic trees of aphids and Buchnera was then measured.  ...  We also investigated the usability of the Buchnera gnd gene as a barcoding marker for aphid identification.  ...  For each dataset, chains were run starting from a random tree and followed by 1 million Markov chain Monte Carlo generations.  ... 
doi:10.1111/j.1365-3113.2012.00647.x fatcat:sccpwfs5ifbtlj5uzh6gywnm3m

Completion for rewriting modulo a congruence [chapter]

Leo Bachmair, Nachum Dershowitz
1987 Lecture Notes in Computer Science  
We present completion methods for rewriting modulo a congruence, generalizing previous methods by Peterson and Stickel (1981) and Jouannaud and Kirchner (1986) .  ...  We formalize our methods as equational inference systems and describe techniques for reasoning about such systems.  ...  Jouannaud and Kirchner (1986) generalized the concept to rewriting modulo a congruence, in general.  ... 
doi:10.1007/3-540-17220-3_17 fatcat:spyymf3dknewxnswap7kk2tjjq

The Systematic Utility of Floral and Vegetative Fragrance in Two Genera of Nyctaginaceae

Rachel A. Levin, Lucinda A. McDade, Robert A. Raguso
2003 Systematic Biology  
in a DNA sequence data set.  ...  profiles were often recovered by analyses of fragrance).  ...  For use of a GC-MS and injection of many of the samples, we thank E. Pichersky and J. D'Auria (University of Michigan). We are grateful for the helpful comments provided by J. G.  ... 
doi:10.1080/10635150309321 fatcat:tw745q4mfrcgzbxqtmwmwzm2ne

The Systematic Utility of Floral and Vegetative Fragrance in Two Genera of Nyctaginaceae

Rachel A. Levin, Lucinda A. McDade, Robert A. Raguso, Roberta Mason-Gamer
2003 Systematic Biology  
in a DNA sequence data set.  ...  profiles were often recovered by analyses of fragrance).  ...  For use of a GC-MS and injection of many of the samples, we thank E. Pichersky and J. D'Auria (University of Michigan). We are grateful for the helpful comments provided by J. G.  ... 
doi:10.1080/10635150390196975 pmid:12775523 fatcat:zgbuu6b2ebcdpatq3uc7jduvhy

Humans and mice fluctuate between external and internal modes of sensory processing [article]

Veith Andreas Weilnhammer, Heiner Stuke, Anna-Lena Eckert, Kai Standvoss, Philipp Sterzer
2021 bioRxiv   pre-print
Here, we asked whether such infra-slow oscillations arise as a noise-related epiphenomenon of limited processing capacity or, alternatively, represent a structured mechanism of perceptual inference.  ...  Between-mode fluctuations may benefit perception by enabling the generation of stable representations of the environment despite an ongoing stream of noisy sensory inputs.  ...  As in humans, autocorrelation coefficients were best fit by an exponential function (adjusted R 2 for stimulus-congruence: 0.44; history-congruence: 0.52) as compared to a linear A.  ... 
doi:10.1101/2021.08.20.457079 fatcat:ua3436wrbna7jfng7kpspgdg4u

Page 1167 of Mathematical Reviews Vol. , Issue 98B [page]

1998 Mathematical Reviews  
The authors consider the problem of linear-time random gener- ation of trees, motivated, for example, by applications in image synthesis.  ...  Summary: “The group of congruences and permutations of the two-colored N-dimensional Boolean cube is considered. The total number of orbits generated by these automorphisms is shown to scale as 2?"  ... 
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