A Computation in a Cellular Automaton Collider Rule 110

A cellular automaton collider is a finite state machine build of rings of one-dimensional cellular automata. We show how a computation can be performed on the collider by exploiting interactions between gliders (particles, localisations). The constructions proposed are based on universality of elementary cellular automaton rule 110, cyclic tag systems, supercolliders, and computing on rings.Comment: 39 pages, 32 figures, 3 table

Simple networks on complex cellular automata: From de Bruijn diagrams to jump-graphs

We overview networks which characterise dynamics in cellular automata. These networks are derived from one-dimensional cellular automaton rules and global states of the automaton evolution: de Bruijn diagrams, subsystem diagrams, basins of attraction, and jump-graphs. These networks are used to understand properties of spatially-extended dynamical systems: emergence of non-trivial patterns, self-organisation, reversibility and chaos. Particular attention is paid to networks determined by travelling self-localisations, or gliders.Comment: 25 pages, 14 figure

Heterogeneous pipelined square-root Kalman Filter algorithm for the MMSE-OSIC problem

The final publication is available at Springer via http://dx.doi.org/10.1007/s11227-009-0354-x[EN] This paper describes a pipelined parallel algorithm for the MMSE-OSIC decoding procedure proposed in V-BLAST wireless MIMO systems, for heterogeneous networks of processors. It is based on a block version of the square-root Kalman Filter algorithm that was initially devised to solve the RLS problem. It has been parallelized in a pipelined way obtaining a good efficiency and scalability. The optimum load balancing for this parallel algorithm is dynamic, but we derive a static load balancing scheme with good performance. © 2009 Springer Science+Business Media, LLC.This work has been supported by the Generalitat Valenciana, project 20080811, by the Universidad Politecnica de Valencia, project 20080009, by the Conserjería de Educacion de la Región de Murcia (Fundacion Séneca, 08763/PI/08), and by the Ministerio de Ciencia e Innovacion (TIN2008-06570-C04-02).Martínez Zaldívar, FJ.; Vidal Maciá, AM.; Giménez Cánovas, D. (2011). Heterogeneous pipelined square-root Kalman Filter algorithm for the MMSE-OSIC problem. Journal of Supercomputing. 58(2):235-243. https://doi.org/10.1007/s11227-009-0354-xS235243582Foschini GJ (1996) Layered space-time architecture for wireless communications in a fading environment when using multiple antennas. Bell Labs Techn J 1:41–59Hassibi B (2000) An efficient square-root algorithm for BLAST. In: IEEE international conference on acoustics, speech and signal processing 2000, vol 2, pp II737–II740Zhu H, Lei Z, Chin FPS (2004) An improved square-root algorithm for BLAST. IEEE Signal Process Lett 11(9)Choi Y-S, Voltz PJ, Cassara FA (2001) On channel estimation and detection for multicarrier signals in fast and selective Rayleigh fading channels. IEEE Trans Commun 49(8)Burg A, Haene S, Perels D, Luethi P, Felber N, Fichtner W (2006) Algorithm and VLSI architecture for linear MMSE detection in MIMO-OFDM systems. In: Proceedings of the IEEE int symp on circuits and systems, May 2006Martínez Zaldívar FJ (2007) Algoritmos paralelos segmentados para los problemas de Mínimos Cuadrados Recursivos (RLS) y de Detección por Cancelación Ordenada y Sucesiva de Interferencia (OSIC). PhD thesis, Facultad de Informática, Universidad Politécnica de Valencia, SpainSayed AH, Kailath T (1994) A state-space approach to adaptive RLS filtering. IEEE Signal Process Mag 11(3):18–60Kumar V, Gram A, Gupta A, Karypis G (2003) An introduction to parallel computing: design and analysis of algorithms, Chap 4, 2nd edn. Addison-Wesley, Harlow

Rationing tests for drug-resistant tuberculosis - who are we prepared to miss?

BACKGROUND: Early identification of patients with drug-resistant tuberculosis (DR-TB) increases the likelihood of treatment success and interrupts transmission. Resource-constrained settings use risk profiling to ration the use of drug susceptibility testing (DST). Nevertheless, no studies have yet quantified how many patients with DR-TB this strategy will miss. METHODS: A total of 1,545 subjects, who presented to Lima health centres with possible TB symptoms, completed a clinic-epidemiological questionnaire and provided sputum samples for TB culture and DST. The proportion of drug resistance in this population was calculated and the data was analysed to demonstrate the effect of rationing tests to patients with multidrug-resistant TB (MDR-TB) risk factors on the number of tests needed and corresponding proportion of missed patients with DR-TB. RESULTS: Overall, 147/1,545 (9.5%) subjects had culture-positive TB, of which 32 (21.8%) had DR-TB (MDR, 13.6%; isoniazid mono-resistant, 7.5%; rifampicin mono-resistant, 0.7%). A total of 553 subjects (35.8%) reported one or more MDR-TB risk factors; of these, 506 (91.5%; 95% CI, 88.9-93.7%) did not have TB, 32/553 (5.8%; 95% CI, 3.4-8.1%) had drug-susceptible TB, and only 15/553 (2.7%; 95% CI, 1.5-4.4%) had DR-TB. Rationing DST to those with an MDR-TB risk factor would have missed more than half of the DR-TB population (17/32, 53.2%; 95% CI, 34.7-70.9). CONCLUSIONS: Rationing DST based on known MDR-TB risk factors misses an unacceptable proportion of patients with drug-resistance in settings with ongoing DR-TB transmission. Investment in diagnostic services to allow universal DST for people with presumptive TB should be a high priority

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data

<p>Abstract</p> <p>Background</p> <p>Illumina's second-generation sequencing platform is playing an increasingly prominent role in modern DNA and RNA sequencing efforts. However, rapid, simple, standardized and independent measures of run quality are currently lacking, as are tools to process sequences for use in downstream applications based on read-level quality data.</p> <p>Results</p> <p>We present SolexaQA, a user-friendly software package designed to generate detailed statistics and at-a-glance graphics of sequence data quality both quickly and in an automated fashion. This package contains associated software to trim sequences dynamically using the quality scores of bases within individual reads.</p> <p>Conclusion</p> <p>The SolexaQA package produces standardized outputs within minutes, thus facilitating ready comparison between flow cell lanes and machine runs, as well as providing immediate diagnostic information to guide the manipulation of sequence data for downstream analyses.</p

Increasing dominance of large lianas in Amazonian forests

Ecological orthodoxy suggests that old-growth forests should be close to dynamic equilibrium, but this view has been challenged by recent findings that neotropical forests are accumulating carbon and biomass, possibly in response to the increasing atmospheric concentrations of carbon dioxide. However, it is unclear whether the recent increase in tree biomass has been accompanied by a shift in community composition. Such changes could reduce or enhance the carbon storage potential of old-growth forests in the long term. Here we show that non-fragmented Amazon forests are experiencing a concerted increase in the density, basal area and mean size of woody climbing plants (lianas). Over the last two decades of the twentieth century the dominance of large lianas relative to trees has increased by 1.7–4.6% a year. Lianas enhance tree mortality and suppress tree growth, so their rapid increase implies that the tropical terrestrial carbon sink may shut down sooner than current models suggest. Predictions of future tropical carbon fluxes will need to account for the changing composition and dynamics of supposedly undisturbed forests

Artificial intelligence prediction of the effect of rehabilitation in whiplash associated disorder.

The active cervical range of motion (aROM) is assessed by clinicians to inform their decision-making. Even with the ability of neck motion to discriminate injured from non-injured subjects, the mechanisms to explain recovery or persistence of WAD remain unclear. There are few studies of ROM examinations with precision tools using kinematics as predictive factors of recovery rate. The present paper will evaluate the performance of an artificial neural network (ANN) using kinematic variables to predict the overall change of aROM after a period of rehabilitation in WAD patients. To achieve this goal the neck kinematics of a cohort of 1082 WAD patients (55.1% females), with mean age 37.68 (SD 12.88) years old, from across Spain were used. Prediction variables were the kinematics recorded by the EBI® 5 in routine biomechanical assessments of these patients. These include normalized ROM, speed to peak and ROM coefficient of variation. The improvement of aROM was represented by the Neck Functional Holistic Analysis Score (NFHAS). A supervised multi-layer feed-forward ANN was created to predict the change in NFHAS. The selected architecture of the ANN showed a mean squared error of 308.07-272.75 confidence interval for a 95% in the Monte Carlo cross validation. The performance of the ANN was tested with a subsample of patients not used in the training. This comparison resulted in a medium correlation with R = 0.5. The trained neural network to predict the expected difference in NFHAS between baseline and follow up showed modest results. While the overall performance is moderately correlated, the error of this prediction is still too large to use the method in clinical practice. The addition of other clinically relevant factors could further improve prediction performance

The use of fluoroproline in MUC1 antigen enables efficient detection of antibodies in patients with prostate cancer

A structure-based design of a new gene22ration tumor-associated glycopeptides with improved affinity against two anti-MUC1 antibodies is described. These unique antigens feature a fluorinated proline residue, such as a (4S)-4-fluoro-L-proline or 4,4-difluoroproline, at the most immunogenic domain. Binding assays using bio-layer interferometry reveal 3-fold to 10-fold affinity improvement with respect to the natural (glyco)peptides. According to X-ray crystallography and MD simulations, the fluorinated residues stabilize the antigen-antibody complex by enhancing key CH/ interactions. Interestingly, a notable improvement in detection of cancer-associated anti-MUC1 antibodies from serum of patients with prostate cancer is achieved with the non-natural antigens, which proves that these derivatives can be considered better diagnostic tools than the natural antigen for this type of cancer.We thank the Ministerio de Economía y Competitividad (projects CTQ2015-67727-R, UNLR13-4E-1931, CTQ2013-44367-C2-2-P, CTQ2015-64597-C2-1P, and BFU2016-75633-P). I. A. B. thanks the Asociación Española Contra el Cancer en La Rioja for a grant. I. S. A. and G. J. L. B. thank FCT Portugal (PhD studentship and FCT Investigator, respectively) and the EPSRC for funding. G. J. L. B. holds a Royal Society URF and an ERC StG (TagIt). F.C. and G. J. L. B thank the EU (Marie-Sklodowska Curie ITN, Protein Conjugates). R.H-G. thanks Agencia Aragonesa para la Investigación y Desarrollo (ARAID) and the Diputación General de Aragón (DGA, B89) for financial support. The research leading to these results has also received funding from the FP7 (2007-2013) under BioStruct-X (grant agreement N°283570 and BIOSTRUCTX_5186). We thank synchrotron radiation source DIAMOND (Oxford) and beamline I04 (number of experiment mx10121-19). Hokkaido University group acknowledges to JSPS KAKENHI Grant Number 25220206 and JSPS Wakate B KAKENHI Grant Number 24710242. We also thank CESGA (Santiago de Compostela) for computer support

Hierarchy Theory of Evolution and the Extended Evolutionary Synthesis: Some Epistemic Bridges, Some Conceptual Rifts

Contemporary evolutionary biology comprises a plural landscape of multiple co-existent conceptual frameworks and strenuous voices that disagree on the nature and scope of evolutionary theory. Since the mid-eighties, some of these conceptual frameworks have denounced the ontologies of the Modern Synthesis and of the updated Standard Theory of Evolution as unfinished or even flawed. In this paper, we analyze and compare two of those conceptual frameworks, namely Niles Eldredge’s Hierarchy Theory of Evolution (with its extended ontology of evolutionary entities) and the Extended Evolutionary Synthesis (with its proposal of an extended ontology of evolutionary processes), in an attempt to map some epistemic bridges (e.g. compatible views of causation; niche construction) and some conceptual rifts (e.g. extra-genetic inheritance; different perspectives on macroevolution; contrasting standpoints held in the “externalism–internalism” debate) that exist between them. This paper seeks to encourage theoretical, philosophical and historiographical discussions about pluralism or the possible unification of contemporary evolutionary biology