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https://www.readbyqxmd.com/read/29276331/wheeler-graphs-a-framework-for-bwt-based-data-structures
#1
Travis Gagie, Giovanni Manzini, Jouni Sirén
The famous Burrows-Wheeler Transform (BWT) was originally defined for a single string but variations have been developed for sets of strings, labeled trees, de Bruijn graphs, etc. In this paper we propose a framework that includes many of these variations and that we hope will simplify the search for more. We first define Wheeler graphs and show they have a property we call path coherence. We show that if the state diagram of a finite-state automaton is a Wheeler graph then, by its path coherence, we can order the nodes such that, for any string, the nodes reachable from the initial state or states by processing that string are consecutive...
October 25, 2017: Theoretical Computer Science
https://www.readbyqxmd.com/read/29243659/comparative-study-of-the-serum-measurement-of-pth-on-roche-cobas-e411%C3%A2-versus-the-abbott-architect-ci8200%C3%A2
#2
Mohammed Bensalah, Ouardia Bouayadi, Nawal Rahmani, Amina Lyagoubi, Somiya Lamrabat, Mohammed Choukri
Parathormone (PTH) is the main hormone of phosphocalcic homeostasis. It is synthesized and secreted by the parathyroid glands. PTH has become a routine test in the medical biology laboratory. However, its measurement presents analytical difficulties with the various marketed kits. The aim of this work is to present the results of a comparative study between the PTH measurment on Abbott architect ci8200 and on Roche's Cobas e411 automaton. It is a prospective study carried out for 252 hospitalized patients in the various departments of the University Hospital Center Mohammed VI of Oujda...
December 15, 2017: Annales de Biologie Clinique
https://www.readbyqxmd.com/read/29241901/comparison-of-timed-automata-with-discrete-event-simulation-for-modeling-of-biomarker-based-treatment-decisions-an-illustration-for-metastatic-castration-resistant-prostate-cancer
#3
Koen Degeling, Stefano Schivo, Niven Mehra, Hendrik Koffijberg, Rom Langerak, Johann S de Bono, Maarten J IJzerman
BACKGROUND: With the advent of personalized medicine, the field of health economic modeling is being challenged and the use of patient-level dynamic modeling techniques might be required. OBJECTIVES: To illustrate the usability of two such techniques, timed automata (TA) and discrete event simulation (DES), for modeling personalized treatment decisions. METHODS: An early health technology assessment on the use of circulating tumor cells, compared with prostate-specific antigen and bone scintigraphy, to inform treatment decisions in metastatic castration-resistant prostate cancer was performed...
December 2017: Value in Health: the Journal of the International Society for Pharmacoeconomics and Outcomes Research
https://www.readbyqxmd.com/read/29209065/cellular-automaton-models-for-time-correlated-random-walks-derivation-and-analysis
#4
J M Nava-Sedeño, H Hatzikirou, R Klages, A Deutsch
Many diffusion processes in nature and society were found to be anomalous, in the sense of being fundamentally different from conventional Brownian motion. An important example is the migration of biological cells, which exhibits non-trivial temporal decay of velocity autocorrelation functions. This means that the corresponding dynamics is characterized by memory effects that slowly decay in time. Motivated by this we construct non-Markovian lattice-gas cellular automata models for moving agents with memory...
December 5, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29195316/computing-aggregate-properties-of-preimages-for-2d-cellular-automata
#5
Randall D Beer
Computing properties of the set of precursors of a given configuration is a common problem underlying many important questions about cellular automata. Unfortunately, such computations quickly become intractable in dimension greater than one. This paper presents an algorithm-incremental aggregation-that can compute aggregate properties of the set of precursors exponentially faster than naïve approaches. The incremental aggregation algorithm is demonstrated on two problems from the two-dimensional binary Game of Life cellular automaton: precursor count distributions and higher-order mean field theory coefficients...
November 2017: Chaos
https://www.readbyqxmd.com/read/29177309/horizontal-drying-fronts-in-films-of-colloidal-dispersions-influence-of-hydrostatic-pressure-and-collective-diffusion
#6
M Nassar, A Gromer, D Favier, F Thalmann, P Hébraud, Y Holl
The origin and time evolution of heterogeneities in drying colloidal films is still a matter of debate. In this work, we studied the behaviour of horizontal drying fronts in a 1D configuration. The effects of hydrostatic pressure and collective diffusion of charged particles, neglected so far, were introduced. We made use of the new simulation tool based on cellular automata we recently presented (Langmuir 2015 & 2017). To check the simulation results, measurements of film profiles in the wet state and drying front velocities were performed with silica colloids...
November 27, 2017: Soft Matter
https://www.readbyqxmd.com/read/29174790/towards-measuring-the-semantic-capacity-of-a-physical-medium-demonstrated-with-elementary-cellular-automata
#7
Peter Dittrich
The organic code concept and its operationalization by molecular codes have been introduced to study the semiotic nature of living systems. This contribution develops further the idea that the semantic capacity of a physical medium can be measured by assessing its ability to implement a code as a contingent mapping. For demonstration and evaluation, the approach is applied to a formal medium: elementary cellular automata (ECA). The semantic capacity is measured by counting the number of ways codes can be implemented...
November 21, 2017: Bio Systems
https://www.readbyqxmd.com/read/29163946/vertebral-body-segmentation-with-growcut-initial-experience-workflow-and-practical-application
#8
Jan Egger, Christopher Nimsky, Xiaojun Chen
Objectives: Spinal diseases are very common; for example, the risk of osteoporotic fracture is 40% for White women and 13% for White men in the United States during their lifetime. Hence, the total number of surgical spinal treatments is on the rise with the aging population, and accurate diagnosis is of great importance to avoid complications and a reappearance of the symptoms. Imaging and analysis of a vertebral column is an exhausting task that can lead to wrong interpretations. The overall goal of this contribution is to study a cellular automata-based approach for the segmentation of vertebral bodies between the compacta and surrounding structures yielding to time savings and reducing interpretation errors...
2017: SAGE Open Medicine
https://www.readbyqxmd.com/read/29124094/a-novel-reversible-logic-gate-and-its-systematic-approach-to-implement-cost-efficient-arithmetic-logic-circuits-using-qca
#9
Peer Zahoor Ahmad, S M K Quadri, Firdous Ahmad, Ali Newaz Bahar, Ghulam Mohammad Wani, Shafiq Maqbool Tantary
Quantum-dot cellular automata, is an extremely small size and a powerless nanotechnology. It is the possible alternative to current CMOS technology. Reversible QCA logic is the most important issue at present time to reduce power losses. This paper presents a novel reversible logic gate called the F-Gate. It is simplest in design and a powerful technique to implement reversible logic. A systematic approach has been used to implement a novel single layer reversible Full-Adder, Full-Subtractor and a Full Adder-Subtractor using the F-Gate...
December 2017: Data in Brief
https://www.readbyqxmd.com/read/29119114/model-checking-temporal-logic-formulas-using-sticker-automata
#10
Weijun Zhu, Changwei Feng, Huanmei Wu
As an important complex problem, the temporal logic model checking problem is still far from being fully resolved under the circumstance of DNA computing, especially Computation Tree Logic (CTL), Interval Temporal Logic (ITL), and Projection Temporal Logic (PTL), because there is still a lack of approaches for DNA model checking. To address this challenge, a model checking method is proposed for checking the basic formulas in the above three temporal logic types with DNA molecules. First, one-type single-stranded DNA molecules are employed to encode the Finite State Automaton (FSA) model of the given basic formula so that a sticker automaton is obtained...
2017: BioMed Research International
https://www.readbyqxmd.com/read/29117100/feature-selection-for-motor-imagery-eeg-classification-based-on-firefly-algorithm-and-learning-automata
#11
Aiming Liu, Kun Chen, Quan Liu, Qingsong Ai, Yi Xie, Anqi Chen
Motor Imagery (MI) electroencephalography (EEG) is widely studied for its non-invasiveness, easy availability, portability, and high temporal resolution. As for MI EEG signal processing, the high dimensions of features represent a research challenge. It is necessary to eliminate redundant features, which not only create an additional overhead of managing the space complexity, but also might include outliers, thereby reducing classification accuracy. The firefly algorithm (FA) can adaptively select the best subset of features, and improve classification accuracy...
November 8, 2017: Sensors
https://www.readbyqxmd.com/read/29081744/predictive-mechanisms-are-not-involved-the-same-way-during-human-human-vs-human-machine-interactions-a-review
#12
REVIEW
Aïsha Sahaï, Elisabeth Pacherie, Ouriel Grynszpan, Bruno Berberian
Nowadays, interactions with others do not only involve human peers but also automated systems. Many studies suggest that the motor predictive systems that are engaged during action execution are also involved during joint actions with peers and during other human generated action observation. Indeed, the comparator model hypothesis suggests that the comparison between a predicted state and an estimated real state enables motor control, and by a similar functioning, understanding and anticipating observed actions...
2017: Frontiers in Neurorobotics
https://www.readbyqxmd.com/read/29076018/climate-change-fisheries-management-and-fishing-aptitude-affecting-spatial-and-temporal-distributions-of-the-barents-sea-cod-fishery
#13
Arne Eide
Climate change is expected to influence spatial and temporal distributions of fish stocks. The aim of this paper is to compare climate change impact on a fishery with other factors impacting the performance of fishing fleets. The fishery in question is the Northeast Arctic cod fishery, a well-documented fishery where data on spatial and temporal distributions are available. A cellular automata model is developed for the purpose of mimicking possible distributional patterns and different management alternatives are studied under varying assumptions on the fleets' fishing aptitude...
December 2017: Ambio
https://www.readbyqxmd.com/read/29064510/biomolecular-computers-with-multiple-restriction-enzymes
#14
Sebastian Sakowski, Tadeusz Krasinski, Jacek Waldmajer, Joanna Sarnik, Janusz Blasiak, Tomasz Poplawski
The development of conventional, silicon-based computers has several limitations, including some related to the Heisenberg uncertainty principle and the von Neumann "bottleneck". Biomolecular computers based on DNA and proteins are largely free of these disadvantages and, along with quantum computers, are reasonable alternatives to their conventional counterparts in some applications. The idea of a DNA computer proposed by Ehud Shapiro's group at the Weizmann Institute of Science was developed using one restriction enzyme as hardware and DNA fragments (the transition molecules) as software and input/output signals...
October 23, 2017: Genetics and Molecular Biology
https://www.readbyqxmd.com/read/29055845/deriving-suitability-factors-for-ca-markov-land-use-simulation-model-based-on-local-historical-data
#15
Xin Fu, Xinhao Wang, Y Jeffrey Yang
Multiple Criteria Evaluation (MCE) is a multi-attributes decision making tool often used in land suitability analysis and land use simulation using Cellular Automata (CA)-Markov model. The goal of this research is to explore the feasibility of using historical data of a study area to select, score, and weight factors quantitatively in the MCE. We have developed logistic regression models fitted by the historical land use changes to select and score each potential factor, and used the Entropy method to determine weights for the selected factors...
October 19, 2017: Journal of Environmental Management
https://www.readbyqxmd.com/read/29039035/temporal-dynamics-of-land-use-land-cover-change-and-its-prediction-using-ca-ann-model-for-southwestern-coastal-bangladesh
#16
M Tauhid Ur Rahman, Faheemah Tabassum, Md Rasheduzzaman, Humayra Saba, Lina Sarkar, Jannatul Ferdous, Syed Zia Uddin, A Z M Zahedul Islam
Change analysis of land use and land cover (LULC) is a technique to study the environmental degradation and to control the unplanned development. Analysis of the past changing trend of LULC along with modeling future LULC provides a combined opportunity to evaluate and guide the present and future land use policy. The southwest coastal region of Bangladesh, especially Assasuni Upazila of Satkhira District, is the most vulnerable to natural disasters and has faced notable changes in its LULC due to the combined effects of natural and anthropogenic causes...
October 17, 2017: Environmental Monitoring and Assessment
https://www.readbyqxmd.com/read/29035805/velocity-of-lateral-drying-fronts-in-film-formation-by-drying-of-colloidal-dispersions-a-2d-simulation
#17
M Nassar, A Gromer, F Thalmann, P Hébraud, Y Holl
Drying of colloids is always heterogeneous and proceeds by progression of drying fronts in various directions at various velocities. The fundamental mechanisms at the origin of appearance and motion of drying fronts are still not totally understood. This article addresses these questions in the case of lateral drying fronts by using the new simulation tool based on cellular automata we recently developed (Langmuir 2015 and 2017). For the first time, a 2D simulation is proposed. Silica dispersions were used as model colloids to test the simulation...
October 4, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28979308/sequential-and-mixed-genetic-algorithm-and-learning-automata-sgala-mgala-for-feature-selection-in-qsar
#18
Habib MotieGhader, Sajjad Gharaghani, Yosef Masoudi-Sobhanzadeh, Ali Masoudi-Nejad
Feature selection is of great importance in Quantitative Structure-Activity Relationship (QSAR) analysis. This problem has been solved using some meta-heuristic algorithms such as GA, PSO, ACO and so on. In this work two novel hybrid meta-heuristic algorithms i.e. Sequential GA and LA (SGALA) and Mixed GA and LA (MGALA), which are based on Genetic algorithm and learning automata for QSAR feature selection are proposed. SGALA algorithm uses advantages of Genetic algorithm and Learning Automata sequentially and the MGALA algorithm uses advantages of Genetic Algorithm and Learning Automata simultaneously...
2017: Iranian Journal of Pharmaceutical Research: IJPR
https://www.readbyqxmd.com/read/28971399/qm-automata-a-new-class-of-restricted-quantum-membrane-automata
#19
Konstantinos Giannakis, Alexandros Singh, Kalliopi Kastampolidou, Christos Papalitsas, Theodore Andronikos
The term "Unconventional Computing" describes the use of non-standard methods and models in computing. It is a recently established field, with many interesting and promising results. In this work we combine notions from quantum computing with aspects of membrane computing to define what we call QM automata. Specifically, we introduce a variant of quantum membrane automata that operate in accordance with the principles of quantum computing. We explore the functionality and capabilities of the QM automata through indicative examples...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28970095/new-statistical-models-of-nonergodic-cognitive-systems-and-their-pathologies
#20
Rodrick Wallace
Cognition most singularly involves choice that reduces uncertainty. Reduction of uncertainty implies the existence of an information source 'dual' to the cognitive process under study. However, information source uncertainty for path-dependent nonergodic systems cannot be described as a conventional Shannon 'entropy' since time averages are not ensemble averages. Nonetheless, the essential nature of information as a form of free energy allows study of nonergodic cognitive systems having complex dynamic topologies whose algebraic expression is in terms of directed homotopy groupoids rather than groups...
January 7, 2018: Journal of Theoretical Biology
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